Purification of polymerase complexes

ABSTRACT

Disclosed are methods for isolating polymerase complexes from a mixture of polymerase complex components. The polymerase complexes can comprise a nanopore to provide isolated nanopore sequencing complexes. The methods relate to the positive and negative isolation of the polymerase complexes and/or nanopore sequencing complexes. Also disclosed is a nucleic acid adaptor for isolating active polymerase complexes, polymerase complexes comprising the nucleic acid adaptor, and methods for isolating active polymerase complexes using the nucleic acid adaptor.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of International Patent ApplicationNo. PCT/EP2016/078781, filed Nov. 25, 2016, which claims benefit ofpriority to U.S. Provisional Patent Application No. 62/373,973, filedAug. 11, 2016, U.S. Provisional Patent Application No. 62/295,010, filedFeb. 13, 2016, and U.S. Provisional Patent Application No. 62/260,194,filed Nov. 25, 2015, the contents of which are herein incorporated byreference in their entireties for all purposes.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted electronically in ASCII format and is hereby incorporated byreference in its entirety. Said ASCII copy, created on Jun. 18, 2018, isnamed SeqList04338527US1.txt and is 1,670 bytes in size.

TECHNICAL FIELD

Disclosed are methods for isolating polymerase complexes that aresubsequently incorporated into membranes of biochips to enable nanoporesequencing of polynucleotides. Also disclosed is a nucleic acid adaptorfor isolating active polymerase complexes, polymerase complexescomprising the nucleic acid adaptor, and methods for isolating activepolymerase complexes using the nucleic acid adaptor.

BACKGROUND

Nanopore biochips are devices that provide single-molecule detection andanalytical capabilities that are achieved by electrophoretically drivingmolecules in solution through a nano-scale pore. The nanopore provides ahighly confined space within which single nucleic acid polymers can beanalyzed at high throughput by one of a variety of means, and theperfect processivity that can be enforced in a narrow pore ensures thatthe native order of the nucleobases in a polynucleotide is reflected inthe sequence of signals that is detected. Kilobase length polymers(single-stranded genomic DNA or RNA) or small molecules (e.g.,nucleosides) can be identified and characterized without amplificationor labeling, a unique analytical capability that makes inexpensive,rapid DNA sequencing a possibility.

DNA polymerases have been used in conjunction with nanopores to controlthe rate of DNA translocation through the nanopore. An enzyme motorcoupled to a nanopore is attractive for two reasons: (1) thepolymerase-DNA complex forms in bulk solution, enabling it to beelectrophoretically captured in the nanopore; (2) relatively slow andcontrolled motion is observed as the polymerase processively steps theDNA molecule through the nanopore.

Progress has been made in providing engineered DNA polymerases withdistinct functions and properties that refine the control of themovement of polynucleotide by the polymerases. However, a challengeremains in fabricating nanopore biochips that provide a high density ofindividually addressable nanopores that are functionally coupled to thepolymerase-polynucleotide complexes.

BRIEF SUMMARY OF THE INVENTION

Disclosed are methods for isolating polymerase complexes from a mixtureof polymerase complex components. The polymerase complexes can comprisea nanopore to provide isolated nanopore sequencing complexes. Themethods relate to the positive and negative isolation of the polymerasecomplexes and/or nanopore sequencing complexes.

In one aspect, a method for isolating an active polymerase complex isprovided. In some embodiments, the method comprises (a) providing areaction mixture comprising unbound polymerase complex components, and aplurality of capture complexes each comprising a polymerase enzyme, apolynucleotide template, and a capture oligonucleotide conjugated to apurification moiety; (b) binding the capture complexes to a solid phasesupport comprising a purification moiety-binding compound; (c) providingreagents comprising nucleotides for enabling template complementarypolynucleotide synthesis by the activity of the polymerase of the activepolymerase complexes to obtain a plurality of active polymerasecomplexes comprising extended complementary sequences; and (d) isolatingthe active polymerase complexes having extended complementary sequencesfrom inactive polymerase complexes comprising unextended complementarysequences, thereby isolating the active polymerase complexes. Theinactive polymerase complexes having unextended complementary sequencesremain bound to the solid phase support, and active polymerase complexeshaving extended complementary sequences are released from the capturecomplex by the activity of the polymerase.

In some embodiments, the polynucleotide template is a linear or acircular template, and the capture complexes each further comprise anoligonucleotide primer. In some embodiments, polynucleotide template isa self-priming template.

In some embodiments, the method further comprises removing unboundpolymerase components from the capture complexes that are bound to thesolid phase support.

In some embodiments, the binding of the capture complex to the solidphase medium is reversible.

In some embodiments, the purification moiety is a biotin or modifiedbiotin, and the purification moiety-binding compound is streptavidin ormodified streptavidin. In some embodiments, the biotin compoundcomprises desthiobiotin or a derivative thereof, and the biotin-bindingcompound comprises streptavidin or a derivative thereof.

In some embodiments, the polymerase is selected from DNA polymerase,reverse transcriptase, and RNA polymerase. In some embodiments, thepolymerase is a wild-type DNA polymerase or variant thereof.

In some embodiments, the isolated polymerase complexes each comprise ananopore. In some embodiments, the nanopore is a wild-type nanopore orvariant thereof. In some embodiments, the nanopore is a wild-type or avariant of an aHL or OmpG nanopore.

In another aspect, a method is provided for positively isolating apolymerase complex. In some embodiments, the method comprises (a)providing a reaction mixture comprising unbound polymerase complexcomponents, and a plurality of capture complexes each comprising apolymerase enzyme, a polynucleotide template, and a captureoligonucleotide comprising a purification moiety; (b) binding thecapture complexes to a solid support comprising a purificationmoiety-binding compound; and (c) isolating the polymerase complexes fromthe polymerase complex components.

In some embodiments, the polynucleotide template is a linear or acontinuous template, and the capture oligonucleotide is a captureoligonucleotide primer. In some embodiments, the polynucleotide templateis a self-priming template, and said self-priming template furthercomprises a purification moiety.

In some embodiments, the method further comprising releasing saidpolymerase-polynucleotide complex from the solid phase support.

In some embodiments, the method further comprises removing unboundpolymerase components from the capture complexes that are bound to thesolid phase support.

In some embodiments, the binding of the capture complex to the solidphase medium is reversible.

In some embodiments, the purification moiety is a biotin or modifiedbiotin, and the purification moiety-binding compound is streptavidin ormodified streptavidin. In some embodiments, the biotin compoundcomprises desthiobiotin or a derivative thereof, and the biotin-bindingcompound comprises streptavidin or a derivative thereof.

In some embodiments, the polymerase is selected from DNA polymerase,reverse transcriptase, and RNA polymerase. In some embodiments, thepolymerase is a wild-type DNA polymerase or variant thereof.

In some embodiments, the isolated polymerase complexes each comprise ananopore. In some embodiments, the nanopore is a wild-type nanopore orvariant thereof. In some embodiments, the nanopore is a wild-type or avariant form of an aHL or OmpG nanopore.

In another aspect, a method is provided for negatively isolating apolymerase complex from a mixed population of unbound polymerase complexcomponents. In some embodiments, the method comprises: (a) providing areaction mixture comprising polymerase complex components, and aplurality of polymerase complexes each comprising a polymerase enzymebound to a polynucleotide template; (b) binding unbound polymeraseenzyme to a capture oligonucleotide comprising a purification moiety toform a capture oligonucleotide polymerase enzyme composite; and (c)binding the capture oligonucleotide polymerase enzyme composite to asolid support comprising a purification moiety-binding compound, therebyisolating the polymerase complexes from the polymerase-polynucleotidecomplex components.

In some embodiments, the binding of the capture complex to the solidphase medium is reversible.

In some embodiments, the capture oligonucleotide is a double strandedpolynucleotide. In some embodiments, the polynucleotide template is alinear or a circular template, and the capture complexes each furthercomprise an oligonucleotide primer. In some embodiments, thepolynucleotide template is a self-priming template.

In some embodiments, the purification moiety is a biotin or modifiedbiotin, and the purification moiety-binding compound is streptavidin ormodified streptavidin. In some embodiments, the biotin compoundcomprises desthiobiotin or a derivative thereof, and the biotin-bindingcompound comprises streptavidin or a derivative thereof.

In some embodiments, the polymerase is selected from DNA polymerase,reverse transcriptase, and RNA polymerase. In some embodiments, thepolymerase is a wild-type DNA polymerase or variant thereof.

In some embodiments, the isolated polymerase complexes each comprise ananopore. In some embodiments, the nanopore is a wild-type nanopore orvariant thereof. In some embodiments, the nanopore is a wild-type or avariant form of an aHL or OmpG nanopore.

In another aspect, a method is provided for preparing a biochip. In someembodiments, the method comprises (a) isolating a polymerase complexaccording to any one of the methods described herein; and (b) attachingthe polymerase complex to a nanopore pre-formed in the membrane of thebiochip to provide a nanopore-polymerase complex. In some embodiments,the membrane has a density of said nanopore sequencing complexes of atleast 500,000 nanopore sequencing complexes 1 mm². In some embodiments,at least 70% of the nanopore-polymerase complexes are functionalnanopore-polymerase complexes.

In other embodiments, the method provided for preparing a biochipcomprises (a) isolating a polymerase complex according to any one of themethods described herein, wherein said polymerase complex furthercomprises a nanopore to provide a nanopore-polymerase complex; and (b)inserting the nanopore-polymerase complex into the membrane of thebiochip. In some embodiments, the membrane has a density of saidnanopore sequencing complexes of at least 500,000 nanopore sequencingcomplexes 1 mm². In some embodiments, at least 70% of thenanopore-polymerase complexes are functional nanopore-polymerasecomplexes.

In another aspect, provided herein is a biochip for sequencingpolynucleotide templates. The biochip comprises an array ofnanopore-polymerase complexes prepared according to any one of themethods described herein.

In another aspect, a method is provided for nanopore sequencing apolynucleotide template. The sequencing method comprises (a) preparing abiochip according to any one of methods described herein; (b) providingtagged nucleotides or nucleotide analogs to the nanopore sequencingcomplex, wherein the tag of the tagged nucleotide is detectable with theaid of the nanopore; (c) carrying out a polymerization reaction with theaid of the polymerase coupled to the nanopore of the nanopore-sequencingcomplex, thereby incorporating an individual nucleotide of the taggednucleotides into a growing strand complementary to a samplepolynucleotide template; and (d) detecting, with the aid of thenanopore, a tag associated with the individual tagged nucleotide duringincorporation of said individual tagged nucleotide, wherein the tag isdetected with the aid of the nanopore while the nucleotide is associatedwith the polymerase, thereby providing a sequence of the nucleic acidsample. In some embodiments, the polynucleotide template is singlestranded DNA. In other embodiments, the polynucleotide template isdouble stranded DNA. In yet other embodiments, the polynucleotidetemplate is RNA.

Nucleic Acid Adaptor for Isolating Active Polymerase Complexes andMethods of Use Thereof

Disclosed is a nucleic acid adaptor for isolating active polymerasecomplexes, polymerase complexes comprising the nucleic acid adaptor, andmethods for isolating active polymerase complexes using the nucleic acidadaptor. The isolated polymerase complexes are subsequently incorporatedinto membranes of biochips to enable nanopore sequencing ofpolynucleotides.

In one aspect, a nucleic acid adaptor for isolating active polymerasecomplexes is provided. In some embodiments, the adaptor has asingle-stranded region comprising a primer recognition sequence, arunway sequence located 5′ to the primer recognition sequence, and apolymerase termination sequence located 5′ to the runway sequence. Insome embodiments, the runway sequence comprises a nucleotide sequencehaving between 2 and 50 contiguous nucleotide bases selected from nomore than three of the four nucleotide bases of adenine, cytosine,guanine, and thymine, where the nucleotide base that is not contained inthe runway sequence is designated as a stop base, and where the runwaysequence functions as a template for polymerase-driven primer extension.In some embodiments, the polymerase termination sequence comprises atleast one stop base that is effective to terminate any suchpolymerase-driven primer extension.

In some embodiments, the runway sequence is between 8 and 12 nucleotidebases in length.

In some embodiments, the polymerase termination sequence is between 1and 10 nucleotide bases in length.

In another aspect, a polymerase complex is provided. In someembodiments, the polymerase complex comprises: a nucleic acid adaptor asdescribed herein; a primer specific to the primer recognition sequenceof the adaptor; and a polymerase enzyme.

In another aspect, a method is provided for isolating active polymerasecomplexes. In some embodiments, the method comprises: (a) providing areaction mixture comprising a polymerase complex as described herein anda nucleic acid sample, where the adaptor of the polymerase complex isligated to said nucleic acid sample; (b) providing a deoxynucleotidetriphosphate (dNTP) mixture comprising only those dNTPs that arecomplementary to the nucleotide bases contained in the runway sequenceof the adaptor, where one or more of the dNTPs is modified to include acapture moiety having affinity to a binding partner; (c) combining thereaction mixture and the dNTP mixture to enable synthesis of apolynucleotide sequence complementary to the runway sequence by theactivity of the polymerase to obtain a plurality of active polymerasecomplexes comprising extended runway complementary sequences havingmodified dNTPs incorporated therein; (d) binding said active polymerasecomplexes to a solid phase support, where the capture moieties of themodified dNTPs are bound to binding partners on the solid phase support;and (e) isolating said active polymerase complexes having extendedrunway complementary sequences from inactive polymerase complexescomprising unextended runway complementary sequences.

In some embodiments, the nucleic acid sample is a DNA or RNA sample.

In some embodiments, the isolating step comprises washing away theinactive polymerase complexes to yield active polymerase complexes boundto the solid phase support.

In some embodiments, the isolating step comprises washing away theinactive polymerase complexes to yield active polymerase complexes boundto the solid phase support, and thereafter eluting the active polymerasecomplexes from the solid phase support.

In some embodiments, the single-stranded region of the adaptor is alinear or a circular template.

In some embodiments, the binding step of the active polymerase complexto the solid phase support is reversible.

In some embodiments, the capture moiety is a biotin or modified biotin,and the binding partner is streptavidin or modified streptavidin. Insome embodiments, the biotin compound comprises desthiobiotin or aderivative thereof, and the binding partner comprises streptavidin or aderivative thereof.

In some embodiments, the polymerase is selected from DNA polymerase,reverse transcriptase, and RNA polymerase. In some embodiments, thepolymerase is a wild-type DNA polymerase or variant thereof.

In some embodiments, the isolated active polymerase complexes eachcomprise a nanopore. In some embodiments, the nanopore is a wild-typenanopore or variant thereof. In some embodiments, the nanopore is awild-type or a variant of an aHL or OmpG nanopore.

In another aspect, a method is provided for preparing a biochip. In someembodiments, the method comprises: (a) isolating an active polymerasecomplex according to any one of the methods described herein; and (b)attaching the active polymerase complex to a nanopore pre-formed in themembrane of said biochip to provide a nanopore-polymerase complex. Insome embodiments, the membrane has a density of said nanopore sequencingcomplexes of at least 500,000 nanopore sequencing complexes 1 mm². Insome embodiments, at least 70% of the nanopore-polymerase complexes arefunctional nanopore-polymerase complexes.

In other embodiments, the method for preparing a biochip comprises: (a)isolating an active polymerase complex according any one of the methodsdescribed herein, where the active polymerase complex further comprisesa nanopore to provide a nanopore-polymerase complex; and (b) insertingsaid nanopore-polymerase complex into the membrane of said biochip. Insome embodiments, the membrane has a density of said nanopore sequencingcomplexes of at least 500,000 nanopore sequencing complexes 1 mm². Insome embodiments, at least 70% of the nanopore-polymerase complexes arefunctional nanopore-polymerase complexes.

In another aspect, provided herein is a biochip for sequencingpolynucleotide templates. The biochip comprises an array ofnanopore-polymerase complexes prepared according to any one of themethods described herein.

In another aspect, a method is provided for nanopore sequencing apolynucleotide template. The sequencing method comprises: (a) preparinga biochip according to any one of methods described herein; (b)providing tagged nucleotides or nucleotide analogs to the nanoporesequencing complex, wherein the tag of the tagged nucleotide isdetectable with the aid of the nanopore; (c) carrying out apolymerization reaction with the aid of the polymerase coupled to thenanopore of the nanopore-sequencing complex, thereby incorporating anindividual nucleotide of the tagged nucleotides into a growing strandcomplementary to a sample polynucleotide template; and (d) detecting,with the aid of the nanopore, a tag associated with the individualtagged nucleotide during incorporation of said individual taggednucleotide, where the tag is detected with the aid of the nanopore whilethe nucleotide is associated with the polymerase, thereby providing asequence of the nucleic acid sample. In some embodiments, thepolynucleotide template is single stranded DNA. In other embodiments,the polynucleotide template is double stranded DNA. In yet otherembodiments, the polynucleotide template is RNA.

BRIEF DESCRIPTION OF THE DRAWINGS

For the purpose of illustrating aspects of the present invention, thereare depicted in the drawings certain embodiments of the invention.However, the invention is not limited to the precise arrangements andinstrumentalities of the embodiments depicted in the drawings. Further,if provided, like reference numerals contained in the drawings are meantto identify similar or identical elements.

The file of this patent contains at least one drawing in color. Copiesof this patent or patent publication with color drawing(s) will beprovided by the Office upon request and payment of the necessary fee.

FIG. 1 depicts three possible nanopore structures that are inserted intoa lipid bilayer from a mixture of nanopore protein, enzyme e.g. DNApolymerase, and substrate template e.g. DNA: bare nanopore (A), nanoporebound to polymerase (B), and nanopore bound to template-bound polymerase(C).

FIG. 2 illustrates the process for obtaining of an active polymerasecomplex by active displacement of a capture oligonucleotide.

FIG. 3 illustrates the formation of a capture complex comprising aself-primed polynucleotide and a capture oligonucleotide.

FIG. 4 illustrates a process for isolating an active polymerase complexfrom a mixture of polymerase complex components.

FIG. 5 illustrates a process for positively isolating a polymerasecomplex from a mixture of polymerase complex components.

FIG. 6 illustrates an embodiment of a process for positively isolating apolymerase complex from a mixture of polymerase complex components.

FIG. 7 illustrates a process for negatively isolating a polymerasecomplex from a mixture of polymerase complex components.

FIG. 8 illustrates a urea gel of various fractions in the isolationprocess of active polymerase complexes. Reference is made to Example 1.

FIG. 9 illustrates a urea gel of various fractions in the process forpositively isolating a polymerase complex. Reference is made to Example2.

FIG. 10 illustrates a urea gel demonstrating the activity of thepolymerase of the complex isolated by the process illustrated in FIG. 8. Reference is made to Example 2.

FIG. 11 illustrates the comparison of the number of nanopores insertedin the membrane of a biochip when: (A) the nanopores are comprised inpreformed polymerase complexes as shown in FIG. 8 ; and when (B) and (C)components of the polymerase complex are admixed and allowed to insertinto the membrane without prior isolation of a pre-formed polymerasecomplex. Reference is made to Example 2.

FIG. 12 illustrates the number of active cells that correspond to thenanopores inserted as shown in FIGS. 10 (A), (B), and (C). Reference ismade to Example 2.

FIG. 13 illustrates the percent sequencing yield obtained for number ofactive cells that correspond to the nanopores inserted as shown in FIGS.10 (A), (B), and (C) relative to the total number of cells present onthe biochip. Reference is made to Example 2.

FIG. 14 illustrates an exemplary current trace of nanopore sequencing apolynucleotide template on a biochip comprising polymerase complexesisolated according to the positive isolation method described herein.The four different bases are shown in four different colors as indicatedby the arrows.

FIG. 15 illustrates one embodiment of a nucleic acid adaptor providedherein for isolating active polymerase complexes. As illustrated, theadaptor is ligated to a sample DNA. The adaptor is also shown to haveprimer annealed to the primer recognition sequence of the adaptor and apolymerase enzyme associated with the adaptor prior to primer extension.Figure discloses SEQ ID NO: 3.

FIG. 16 illustrates one embodiment of a nucleic acid adaptor providedherein for isolating active polymerase complexes. As illustrated, theadaptor is ligated to a sample DNA. The adaptor is also shown to haveprimer annealed to the primer recognition sequence of the adaptor and anextended sequence complementary to the runway sequence. Also shown is apolymerase enzyme associated with the adaptor. FIG. 16 discloses SEQ IDNOs:3 and 4, respectively, in order of appearance.

FIG. 17 illustrates one embodiment of a nucleic acid adaptor providedherein for isolating active polymerase complexes. As illustrated, theadaptor is ligated to a sample DNA. The adaptor is linear and is alsoshown to have primer annealed to the primer recognition sequence of theadaptor. Embodiment (1) illustrates the adaptor before enrichmentextension of the runway sequence. Embodiment (2) illustrates the adaptorafter enrichment extension of the runway sequence. FIG. 17 discloses SEQID NO:5.

DETAILED DESCRIPTION

The invention will now be described in detail by way of reference onlyusing the following definitions and examples. All patents andpublications, including all sequences disclosed within such patents andpublications, referred to herein are expressly incorporated byreference.

Unless defined otherwise herein, all technical and scientific terms usedherein have the same meaning as commonly understood by one of ordinaryskill in the art to which this invention belongs. Singleton, et al.,DICTIONARY OF MICROBIOLOGY AND MOLECULAR BIOLOGY, 2D ED., John Wiley andSons, New York (1994), and Hale & Marham, THE HARPER COLLINS DICTIONARYOF BIOLOGY, Harper Perennial, N.Y. (1991) provide one of skill with ageneral dictionary of many of the terms used in this invention. Althoughany methods and materials similar or equivalent to those describedherein can be used in the practice or testing of the present invention,the preferred methods and materials are described. Practitioners areparticularly directed to Sambrook et al., 1989, and Ausubel F M et al.,1993, for definitions and terms of the art. It is to be understood thatthis invention is not limited to the particular methodology, protocols,and reagents described, as these may vary.

Numeric ranges are inclusive of the numbers defining the range. The termabout is used herein to mean plus or minus ten percent (10%) of a value.For example, “about 100” refers to any number between 90 and 110.

Unless otherwise indicated, nucleic acids are written left to right in5′ to 3′ orientation; amino acid sequences are written left to right inamino to carboxy orientation, respectively.

The headings provided herein are not limitations of the various aspectsor embodiments of the invention, which can be had by reference to thespecification as a whole. Accordingly, the terms defined immediatelybelow are more fully defined by reference to the specification as awhole.

All patents and publications, including all sequences disclosed withinsuch patents and publications, referred to herein are expresslyincorporated by reference.

Methods for nanopore sequencing of polymers e.g. polynucleotides andproteins, require enzyme-nanopore-polymer complexes positioned in amembrane e.g. a lipid bilayer, of a biochip.

Current methods for providing an enzyme-nanopore-polymer complexcomprise incubating nanopore protein, polymer, and enzyme to allowassociation of the components, flowing the reaction mixture onto amembrane, and either actively or passively reconstituting the resultingstructures into the membrane. The three possible structures that becomeinserted into the membrane are: the nanopore alone, the nanoporeassociated with the enzyme, and the nanopore associated with the enzymeand polymer. For example, as shown in FIG. 1 , flowing a reactionmixture (100) of nanopore (101) comprising an attachment component(102), polymerase enzyme (Pol) (103) comprising an attachment component(104), and polynucleotide (105) onto a lipid bilayer under conditionsthat will cause the nanopore to insert into the bilayer, e.g.electroporation, will result in (A) the nanopore alone being insertedinto the bilayer, (B) the nanopore associated with the polymerase(enzyme-nanopore complex) being inserted into the bilayer, and (C) thenanopore-polymerase-polynucleotide template e.g. DNA, complex beinginserted into the bilayer. Electroporation efficiency i.e. theefficiency of the process whereby diffusion ofnanopore-polymerase-polynucleotide complexes diffuse to and are insertedinto a membrane depends on the size of the nanopore complex. The largerthe complex, the less the electroporation efficiency. Thus, of the threepossible structures shown in FIG. 1 , the nanopore alone (A) willdiffuse more readily into the membrane than (B) nanopore-polymerasecomplex, which in turn, will diffuse more readily than (C) thenanopore-polymerase-polynucleotide complex. Efficiency will depend onthe size-to-charge ratio of the complex. Structures A and B arenon-functional as neither comprises all three components that arenecessary to determine the sequence of the polymer e.g. DNA.Furthermore, A and B will occupy space on a biochip thereby diminishingthe density of functional enzyme-nanopore-polymer complexes on abiochip. Additionally, at least a portion of the complexes havingstructure C will comprise polymerase enzyme that may not be active.Electroporation may be efficient in any size, but diffusion is believedto bring molecules to the membrane surface so that electroporationlowers the energy needed for the pore to enter the bilayer.

Provided herein are methods for selecting/isolatingpolymerase-polynucleotide complexes i.e. polymerase complexes, frommixtures of unbound complex components to minimize the formation ofincomplete and/or inactive polymerase complexes in lipid bilayers, andthereby increase the efficiency of nanopore sequencing methods. Themethods provided herein can be used to isolate polymerase complexes,which can be subsequently attached to nanopores inserted into themembrane of a biochip to form nanopore sequencing complexes.Additionally, the methods provided herein can be used to isolatepolymerase complexes that further comprise a nanopore attached to thepolymerase to form nanopore sequencing complexes that can subsequentlyinserted into the membrane of a biochip.

Definitions:

The term “dNTP” refers to deoxynucleoside triphosphates. The purinebases (Pu) include adenine (A), guanine (G) and derivatives and analogsthereof. The pyrimidine bases (Py) include cytosine (C), thymine (T),uracil (U) and derivatives and analogs thereof. Examples of suchderivatives or analogs, by way of illustration and not limitation, arethose which are modified with a reporter group, biotinylated, aminemodified, radiolabeled, alkylated, and the like and also includephosphorothioate, phosphite, ring atom modified derivatives, and thelike. The reporter group can be a fluorescent group such as fluorescein,a chemiluminescent group such as luminol, a terbium chelator such asN-(hydroxyethyl) ethylenediaminetriacetic acid that is capable ofdetection by delayed fluorescence, and the like.

The term “polymerase complex” herein refers to a complex formed by theassociation of a polymerase enzyme and a polynucleotide templatesubstrate. Polynucleotide templates that are not self-priming requireoligonucleotide primers to initiate strand extension. Accordingly,absent a self-priming polynucleotide, a polymerase complex can furtherinclude an oligonucleotide primer.

The term “active polymerase complex” herein refers to a complex thatcomprises an active polymerase capable of strand extension and apolynucleotide template. The active polymerase complex can furthercomprise a nanopore that is linked to the active polymerase to providean active nanopore sequencing complex.

The term “nanopore sequencing complex” herein refers to a complex formedby association of a polymerase enzyme, a polynucleotide templatesubstrate, and a nanopore. Polynucleotide templates that are notself-priming require oligonucleotide primers to initiate strandextension. Accordingly, absent a self-priming polynucleotide, a nanoporesequencing complex can further include an oligonucleotide primer.

The term “capture oligonucleotide” herein refers to an oligonucleotidethat comprises a purification moiety that serves to immobilizepolymerase complexes, nanopore sequencing complexes, or unboundpolymerase and polymerase nanopore complexes to a solid support.Preferably, the purification moiety can be biotin or modified biotin,which binds to a purification moiety-binding partner e.g. streptavidinor modified streptavidin, on the solid support.

The term “functional” when used in reference to a nanopore sequencingcomplex, herein refers to a complex of three components: a nanoporeinserted in a membrane, a polymer associated with an enzyme, and thepolymer-associated enzyme that is attached to the nanopore in themembrane. The functional nanopores sequencing complex detects componentsof a sequence e.g. nucleotide bases of a polynucleotide.

The term “polymerase” herein refers to an enzyme that catalyzes thepolymerization of nucleotide (i.e., the polymerase activity). The termpolymerase encompasses DNA polymerases, RNA polymerases, and reversetranscriptases. A “DNA polymerase” catalyzes the polymerization ofdeoxynucleotides. An “RNA polymerase” catalyzes the polymerization ofribonucleotides. A “reverse transcriptase” catalyzes the polymerizationof deoxynucleotides that are complementary to an RNA template.

The terms “polynucleotide” and “nucleic acid” are herein usedinterchangeably to refer to RNA, single stranded DNA (ssDNA), doublestranded DNA (dsDNA), and cDNA molecules.

The term “template DNA molecule” herein refers to a strand of a nucleicacid from which a complementary nucleic acid strand is synthesized by aDNA polymerase, for example, in a primer extension reaction.

The term “sample polynucleotide” herein refers to a polynucleotideobtained from a sample e.g. a biological sample.

The term “template-dependent manner” refers to a process that involvesthe template dependent extension of a primer molecule (e.g., DNAsynthesis by DNA polymerase). The term “template-dependent manner”typically refers to polynucleotide synthesis of RNA or DNA wherein thesequence of the newly synthesized strand of polynucleotide is dictatedby the well-known rules of complementary base pairing (see, for example,Watson, J. D. et al., In: Molecular Biology of the Gene, 4th Ed., W. A.Benjamin, Inc., Menlo Park, Calif. (1987)).

The term “self-priming” herein refers to a polynucleotide template thatgenerates a self-complementary sequence that can act as a primer fortemplate-dependent extension by a polymerase e.g. a DNA polymerase. Ahairpin template is an example of a self-priming template.

The term “nanopore” or “pore” as used herein, generally refers to apore, channel or passage formed or otherwise provided in a membrane. Amembrane may be an organic membrane, such as a lipid bilayer, or asynthetic membrane, such as a membrane formed of a polymeric material.The membrane may be a polymeric material. The nanopore may be disposedadjacent or in proximity to a sensing circuit or an electrode coupled toa sensing circuit, such as, for example, a complementary metal-oxidesemiconductor (CMOS) or field effect transistor (FET) circuit. In someexamples, a nanopore has a characteristic width or diameter on the orderof 0.1 nanometers (nm) to about 1000 nm. Some nanopores are proteins.Alpha-hemolysin is an example of a protein nanopore.

The term “monomeric nanopore” herein refers to a nanopore protein thatconsists of a single subunit.

The term “oligomeric nanopore” herein refers to nanopores that can becomposed of multiple identical subunits, multiple distinct subunits, ora mixture of identical and distinct subunits. Nanopores with identicalsubunits are termed “homo-oligomeric nanopores”. Nanopores containingtwo or more distinct polypeptide subunits are termed “hetero-oligomericnanopores”.

The term “wild-type” herein refers to a gene or gene product that hasthe characteristics of that gene or gene product when isolated from anaturally occurring source.

The term “variant” herein refers to a modified protein which displaysaltered characteristics when compared to the parental protein, e.g.,altered ionic conductance, altered time to thread, etc.

The term “modified variant” herein refers to a variant protein that hasbeen further modified to alter its physical interaction with otherproteins. For example, a modified variant protein may be a multimericvariant nanopore that has been further mutated to affect inter-subunitinteractions.

The term “time to thread” or “TTT” herein refers to the time it takesthe polymerase-tag complex to thread the tag into the nanopore.

The terms “noise” and “ionic current noise” are herein usedinterchangeably and refer to random fluctuations of electrical signal,which include current fluctuations contributed by spontaneous gating andcurrent fluctuations contributed by the inherent architecture of thenanopore. For example, the tertiary make-up of the nanopore can comprisemore than one recognition site for the analyte that is being sensed bythe nanopore thereby inducing additional signals that contribute to theoverall noise of the channel.

The term “constriction amino acids” herein refers to the amino acidsthat determine the size of a nanopore at the constriction zone. Theconstriction zone may be the same as the constriction zone of thewild-type nanopore or it may be a constriction zone introduced viaprotein engineering, or by the introduction of a molecular adapter.

The terms “alpha-hemolysin,” “α-hemolysin,” “aHL,” “aHL,” “α-HL” and“α-HL” are used interchangeably and herein refer to a protein thatself-assembles into a heptameric water-filled transmembrane channel frommonomers, concatemers of monomers, or a combination of monomers andconcatemers of monomers.

The term “attachment component” herein refers to a structure e.g. alinker, which attaches the enzyme e.g. a polymerase, of anenzyme-polymer complex e.g. polymerase complex to a nanopore.

The terms “polynucleotide template” and “polynucleotide substratetemplate” herein refer to a polynucleotide molecule from which acomplementary nucleic acid strand is synthesized by a polynucleotidepolymerase e.g. DNA polymerase. The polynucleotide template can belinear, hairpin, or continuous. Continuous templates can be circular ordumbbell. Hairpin templates can be self-priming templates.

The term “polymerase complex components” herein refers to unboundcomponents required to form a polymerase complex. The components includea polynucleotide template and a polymerase, and can further include anoligonucleotide primer, and/or a nanopore.

The term “isolated” herein refers to a polymerase complex or a nanoporesequencing complex that is separated from at least one of its unboundcomponents from which it is ordinarily formed.

The term “purified” herein refers to a molecule that is present in asample at a concentration of at least 95% by weight, or at least 98% byweight of the sample in which it is contained.

The term “purifying” generally refers to subjecting a polymerase complexor a nanopore sequencing complex to biochemical purification by affinitychromatography.

The term “nucleotide” herein refers to a monomeric unit of DNA or RNAconsisting of a sugar moiety (pentose), a phosphate, and a nitrogenousheterocyclic base. The base is linked to the sugar moiety via theglycosidic carbon (1′ carbon of the pentose) and that combination ofbase and sugar is a nucleoside. When the nucleoside contains a phosphategroup bonded to the 3′ or 5′ position of the pentose it is referred toas a nucleotide. A sequence of operatively linked nucleotides istypically referred to herein as a “base sequence” or “nucleotidesequence,” and is represented herein by a formula whose left to rightorientation is in the conventional direction of 5′-terminus to3′-terminus.

The term “modified nucleotide” herein refers to a nucleotide analog or atagged nucleotide.

The term “nucleotide analog” herein refers to analogs of nucleosidetriphosphates, e.g., (S)-Glycerol nucleoside triphosphates (gNTPs) ofthe common nucleobases: adenine, cytosine, guanine, uracil, andthymidine (Horhota et al.

Organic Letters, 8:5345-5347 [2006]).

The term “tag” herein refers to a detectable moiety that may be atoms ormolecules, or a collection of atoms or molecules. A tag may provide anoptical, electrochemical, magnetic, or electrostatic (e.g., inductive,capacitive) signature, which may be detected with the aid of a nanopore.

The phrase “positively isolating” herein refers to a process ofisolating a polymerase complex or a nanopore sequencing complex bybinding the complex to a solid phase support, and removing unboundcomponents.

The phrase “negatively isolating” herein refers to a process ofisolating polymerase complex components from a reaction mixturecomprising polymerase complexes and polymerase complex components, andbinding the components to a solid phase support thereby isolating thepolymerase complexes.

The term “biotin” as used herein are intended to refer to biotin(cishexahydro-2oxo-1H-thieno[3,4]imidazole-4-pentanoic acid) and anybiotin derivatives and analogs. Such derivatives and analogues aresubstances which form a complex with the biotin binding pocket of nativeor modified streptavidin or avidin. Such compounds include, for example,iminobiotin, desthiobiotin and streptavidin affinity peptides, and alsoinclude biotin-.epsilon.-N-lysine, biocytin hydrazide, amino orsulfhydryl derivatives of 2-iminobiotin and biotinyl-ε-aminocaproicacid-N-hydroxysuccinimide ester, sulfo-succinimide-iminobiotin,biotinbromoacetylhydrazide, p-diazobenzoyl biocytin,3-(N-maleimidopropionyl) biocytin. A preferred derivative of biotin tobe used in the present invention is desthiobiotin or its derivativeDSB-X Biotin, commercially available from Molecular Probes, Eugene,Oreg., USA; product number D20658)

The term “biotinylated” herein refers to a conjugate of modified biotinor biotin analogues with other moieties such as purification moietiese.g. nucleic acid molecules (including single or double stranded DNA,RNA, DNA/RNA chimeric molecules, nucleic acid analogs and any moleculewhich contains or incorporates a nucleotide sequence e.g., a peptidenucleic acid (PNA) or any modification thereof), proteins (includingglycoproteins, enzymes, peptides library or display products andantibodies or derivatives thereof), peptides, carbohydrates orpolysaccharides, lipids, etc., wherein the moieties are covalentlylinked to the modified biotin or biotin analogues. Many biotinylatedligands are commercially available or can be prepared by standardmethods. Processes for coupling a biomolecule, e.g. a nucleic acidmolecule or a protein molecule, to biotin are well known in the art(Bayer and Wilchek, Methods in Molec. Biology 10, 143. 1992).

The term “binding partner” is defined as any biological or other organicmolecule capable of specific or non-specific binding or interaction withanother biological molecule, which binding or interaction may bereferred to as “ligand” binding or interaction and is exemplified by,but not limited to, antibody/antigen, antibody/hapten, enzyme/substrate,enzyme/inhibitor, enzyme/cofactor, binding protein/substrate, carrierprotein/substrate, lectin/carbohydrate, receptor/hormone,receptor/effector or repressor/inducer bindings or interactions. Theterm “binding partner” herein refers to the partners of an affinitycomplex e.g. modified biotin-modified biotin binding partner, used inthe isolation methods described herein.

The term “conjugate” as used herein refer to any conjugate comprising abiotin compound and a biotin-binding compound, in which the biotincompound and biotin-binding compound are linked by non-covalent bonding.Typically, biotin will be bound or linked to one or more, preferablyone, biological or chemical entity, e.g. a biomolecule. As explainedabove, such biotin compounds containing biotin linked to other entitiesare also referred to herein as “biotinylated” purification moieties.

The term “biotin-binding” compound as used herein is intended toencompass any compound which is capable of tightly but non-covalentlybinding to biotin or any biotin compound. Preferred biotin-bindingcompounds include modified streptavidin and avidin, as well asderivatives and analogues thereof e.g. nitro-streptavidin.

The term “avidin” as used herein refers to the native egg-whiteglycoprotein avidin as well as derivatives or equivalents thereof, suchas deglycosylated or recombinant forms of avidin, for example, N-acylavidins, e.g., N-acetyl, N-phthalyl and N-succinyl avidin, and thecommercial products ExtrAvidin, Neutralite Avidin and CaptAvidin

The term “streptavidin” as used herein refers to bacterial streptavidinsproduced by selected strains of Streptomyces, e.g., Streptomycesavidinii, as well as derivatives or equivalents thereof such asrecombinant and truncated streptavidin, such as, for example, “core”streptavidin.

The terms “reversible” and “releasable” are used herein interchangeablyand are intended to mean physical separation or detachment ordissociation of the partners of an affinity complex e.g. modifiedbiotin-modified biotin binding partner. What is required, is that thelinkage between the modified biotin and the modified biotin-bindingpartner is disrupted or broken to allow separation of the respectiveentities.

The term “displacer” herein refers to a molecule (for example, freebiotin) that may physically break or destabilize the linkage betweenpartners of an affinity complex e.g. modified biotin-modified biotinbinding partner, in a sufficient manner to allow it to be cleaved, orreversed, thus allowing the two linked entities to be separated.

The terms “runway” or “runway sequence” herein refer to a nucleotidesequence that is composed of three of the four nucleotides (i.e., anycombination of three nucleotides selected from A, T, G, and C). Thisrunway section can be 3 to 50 bases long, preferably 8 to 12 bases.

In one aspect, the present invention provides a method for isolatingactive polymerase complexes, said method comprising:

-   -   (a) providing a reaction mixture comprising unbound polymerase        complex components, and a plurality of capture complexes each        comprising a polymerase enzyme, a polynucleotide template, and a        capture oligonucleotide conjugated to a purification moiety;    -   (b) binding said capture complexes to a solid phase support        comprising a purification moiety-binding compound;    -   (c) providing reagents comprising nucleotides for enabling        template complementary polynucleotide synthesis by the activity        of the polymerase of said active polymerase complexes to obtain        a plurality of active polymerase complexes comprising extended        complementary sequences; and    -   (d) isolating said active polymerase complexes having extended        complementary sequences from inactive polymerase complexes        comprising unextended complementary sequences and capture        oligonucleotides, thereby isolating said active polymerase        complexes from said polymerase complex components.

The inactive polymerase complexes having unextended complementarysequences may remain bound to said solid phase support, and activepolymerase complexes having extended complementary sequences may bereleased from said capture complex by the activity of said polymerase.

In a second aspect, the present invention provides a method forpositively isolating a polymerase complex, said method comprising:

-   -   (a) providing a reaction mixture comprising unbound polymerase        complex components, and a plurality of capture complexes each        comprising a polymerase enzyme, a polynucleotide template, and a        capture oligonucleotide comprising a purification moiety;    -   (b) binding said capture complexes to a solid support comprising        a purification moiety-binding compound;    -   and    -   (c) isolating said polymerase complexes from said polymerase        complex components.

Said polynucleotide template may be a linear or a continuous template,and the capture oligonucleotide may be a capture oligonucleotide primer.Said template may also be a self-priming template, and said self-primingtemplate further comprises a purification moiety. The method may alsocomprise a step of, further comprising releasing saidpolymerase-polynucleotide complex from said solid phase support.

In a third aspect, the present invention provides a method fornegatively isolating a polymerase complex from a mixed population ofunbound polymerase complex components, said method comprising:

-   -   (a) providing a reaction mixture comprising polymerase complex        components, and a plurality of polymerase complexes each        comprising a polymerase enzyme bound to a polynucleotide        template;    -   (b) binding unbound polymerase enzyme to an optionally double        stranded capture oligonucleotide comprising a purification        moiety to form a capture oligonucleotide polymerase enzyme        composite; and    -   (c) binding said capture oligonucleotide polymerase enzyme        composite to a solid support comprising a purification        moiety-binding compound,        thereby isolating said polymerase complexes from said        polymerase-polynucleotide complex components.

The polynucleotide template according to the methods above may be alinear or a circular template, and the capture complexes may eachfurther comprise an oligonucleotide primer. The polynucleotide templatealso be a self-priming template. The methods above may further comprisea step of removing unbound polymerase components from said capturecomplexes bound to said solid phase support. The binding of said capturecomplex to said solid phase medium may be reversible. The purificationmoiety may be a biotin or modified biotin, and said purificationmoiety-binding compound may be streptavidin or modified streptavidin.Said biotin compound may comprise desthiobiotin or a derivative thereof,and said biotin-binding compound may comprise streptavidin or aderivative thereof. The polymerase may be a DNA polymerase, a reversetranscriptase or a RNA polymerase either as a wild-type DNA polymeraseor as a variant thereof. The isolated polymerase complexes may eachcomprise a nanopore, which may be a wild-type nanopore or variantthereof such as a wild-type or a variant of an aHL or OmpG nanopore.

In a fourth aspect, the present invention provides a method forpreparing a biochip, said method comprising:

-   -   (a) isolating a polymerase complex according to any one of the        methods disclosed above, and    -   (b) attaching said polymerase complex to a nanopore pre-formed        in the membrane of said biochip to provide a nanopore-polymerase        complex, or    -   (b) inserting said nanopore-polymerase complex into the membrane        of said biochip.

Said membrane may have a density of said nanopore sequencing complexesof at least 500,000 nanopore sequencing complexes 1 mm². At least 70% ofthe nanopore-polymerase complexes are functional nanopore-polymerasecomplexes.

The biochip may be a biochip for sequencing polynucleotide templatescomprising an array of nanopore-polymerase complexes prepared asdisclosed above.

In a fifth aspect, the present invention provides a method for nanoporesequencing a polynucleotide template, comprising:

-   -   (a) preparing a biochip;    -   (b) providing tagged nucleotides or nucleotide analogs to said        nanopore sequencing complex, wherein the tag of said tagged        nucleotide is detectable with the aid of said nanopore;    -   (c) carrying out a polymerization reaction with the aid of said        polymerase coupled to said nanopore in said nanopore-sequencing        complex, thereby incorporating an individual tagged nucleotide        of said tagged nucleotides into a growing strand complementary        to a sample polynucleotide template; and    -   (d) detecting, with the aid of said nanopore, a tag associated        with said individual tagged nucleotide during incorporation of        said individual tagged nucleotide, wherein said tag is detected        with the aid of said nanopore while said nucleotide is        associated with said polymerase, thereby providing a sequence of        said nucleic acid sample.

The polynucleotide template may be single stranded DNA, double strandedDNA, or RNA.

In a sixth aspect, the present invention provides a nucleic acid adaptorfor isolating active polymerase complexes, said adaptor having asingle-stranded region comprising a primer recognition sequence, arunway sequence located 5′ to the primer recognition sequence, and apolymerase termination sequence located 5′ to the runway sequence,

-   -   wherein said runway sequence comprises a nucleotide sequence        having between 2 and 50 contiguous nucleotide bases selected        from no more than three of the four nucleotide bases of adenine,        cytosine, guanine, and thymine, wherein the nucleotide base that        is not contained in the runway sequence is designated as a stop        base, and wherein said runway sequence functions as a template        for polymerase-driven primer extension, and    -   wherein said polymerase termination sequence comprises at least        one stop base that is effective to terminate any such        polymerase-driven primer extension.

The runway sequence may be between 8 and 12 nucleotide bases in length,whereas the polymerase termination sequence may be between 1 and 10nucleotide bases in length.

The nucleic acid adaptor may be part of a polymerase complex furthercomprising a primer specific to the primer recognition sequence of theadaptor; and a polymerase enzyme.

In a seventh aspect, the present invention provides a method forisolating active polymerase complexes, said method comprising:

-   -   (a) providing a reaction mixture comprising a polymerase complex        isolated as disclosed above and a nucleic acid DNA or RNA        sample, wherein the adaptor of the polymerase complex is ligated        to said nucleic acid sample;    -   (b) providing a deoxynucleotide triphosphate (dNTP) mixture        comprising only those dNTPs that are complementary to the        nucleotide bases contained in the runway sequence of the        adaptor, wherein one or more of the dNTPs is modified to include        a capture moiety having affinity to a binding partner;    -   (c) combining the reaction mixture and the dNTP mixture to        enable synthesis of a polynucleotide sequence complementary to        the runway sequence by the activity of the polymerase to obtain        a plurality of active polymerase complexes comprising extended        runway complementary sequences having modified dNTPs        incorporated therein;    -   (d) binding said active polymerase complexes to a solid phase        support, wherein the capture moieties of the modified dNTPs are        bound to binding partners on the solid phase support; and    -   (e) isolating said active polymerase complexes having extended        runway complementary sequences from inactive polymerase        complexes comprising unextended runway complementary sequences.

The method may comprise a step of washing away the inactive polymerasecomplexes to yield active polymerase complexes bound to the solid phasesupport. Thereafter, the active polymerase complexes may be eluted fromthe solid phase support. Said single-stranded region of the adaptor maybe a linear or a circular template. Binding of said active polymerasecomplex to said solid phase support may be reversible. The capturemoiety may be a biotin or modified biotin, and said binding partner maybe streptavidin or modified streptavidin. For example, said biotincompound may comprise desthiobiotin or a derivative thereof, and saidbinding partner may comprises streptavidin or a derivative thereof. Thepolymerase is wildtype or variant DNA polymerase, reverse transcriptase,or a RNA polymerase. The isolated active polymerase complexes may eachcomprise a wild-type nanopore or variant thereof, for example awild-type or a variant of an aHL or OmpG nanopore.

In an eighth aspect, the present invention provides a method forpreparing a biochip, comprising the steps of

-   -   (a) isolating an active polymerase complex as disclosed above;        and    -   (b) attaching said active polymerase complex to a nanopore pre        formed in the membrane of said biochip to provide a        nanopore-polymerase complex or    -   (b) inserting said nanopore-polymerase complex into the membrane        of said biochip.

The membrane may have a density of said nanopore sequencing complexes ofat least 500,000 nanopore sequencing complexes 1 mm². At least 70% ofthe nanopore-polymerase complexes should bew functionalnanopore-polymerase complexes.

The present invention is also directed to a biochip for sequencingpolynucleotide templates, comprising an array of nanopore-polymerasecomplexes prepared as disclosed above.

In a final aspect, the present invention provides a method for nanoporesequencing a polynucleotide template, said method comprising:

-   -   (a) preparing a biochip as disclosed above;    -   (b) providing tagged nucleotides or nucleotide analogs to said        nanopore sequencing complex, wherein the tag of said tagged        nucleotide is detectable with the aid of said nanopore;    -   (c) carrying out a polymerization reaction with the aid of said        polymerase coupled to said nanopore in said nanopore-sequencing        complex, thereby incorporating an individual tagged nucleotide        of said tagged nucleotides into a growing strand complementary        to a sample polynucleotide template; and    -   (d) detecting, with the aid of said nanopore, a tag associated        with said individual tagged nucleotide during incorporation of        said individual tagged nucleotide, wherein said tag is detected        with the aid of said nanopore while said nucleotide is        associated with said polymerase, thereby providing a sequence of        said nucleic acid sample.

The polynucleotide template may be double stranded DNA, is singlestranded DNA or RNA.

Methods for Isolating Polymerase Complexes and/or Nanopore SequencingComplexes:

Displacement Purification—Method for Isolating Active PolymeraseComplexes and/or Active Nanopore Sequencing Complexes:

In one aspect, a method is provided for preparing an active nanoporesequencing complex comprising an active polymerase associated with apolynucleotide template i.e. an active polymerase complex. In someembodiments, the active polymerase of the polymerase complex is bound toa nanopore. The active nanopore complex is formed by the binding of itscomponents that are provided as a mixture. The active polymerase complexcomprises a polymer template substrate e.g. a polynucleotide template,and an active polymerase bound to the template. The active polymerasecomplex can further comprise a nanopore that is bound to the activepolymerase. The formed active polymerase complex is subsequentlyisolated from the mixture of unbound polymerase complex components, andinactive polymerase complexes. Unbound polymerase components comprisedistinct polymerase enzyme molecules, template molecules, and nanoporeproteins, and nanopore proteins that have associated with polymeraseenzyme, but not with template molecules. Active polymerase complexes areisolated from inactive polymerase complexes by the ability of thepolymerase to incorporate nucleotides into a polynucleotide strand in atemplate-dependent sequence, which displaces a capture oligonucleotidethat is hybridized to the polynucleotide template. The process ofpolymerase-dependent displacement of a capture oligonucleotide from thepolynucleotide template is illustrated in FIG. 2 .

FIG. 2 illustrates a polymerase complex that comprises a self-primingtemplate (201) and a polymerase (202) bound to the double strandedportion of the self-priming template. In a first step (i), thepolymerase complex combines with a capture oligonucleotide (203), whichcomprises a polynucleotide (204) and a purification moiety (205), toform a capture complex (206) in step (ii). The capture complex istethered/bound to a solid phase (207) by means of the purificationmoiety of the capture oligonucleotide (203) in step (iii). Theinteraction of the capture oligonucleotide with the polymerase complexoccurs by hybridization of sequences on the template and theoligonucleotide. Under catalytic conditions comprising nucleotides andMgCl₂, in step (iv), the active polymerase (208) extends theself-priming template, which as it reaches the bound captureoligonucleotide, displaces the capture oligonucleotide from the capturecomplex as shown in step (v). The free capture oligonucleotide (203)remains bound to the solid phase support, and the active polymerasecomplex (209) is isolated from inactive polymerase complexes andreleased capture oligonucleotides. An inactive polymerase complex failsto extend the self-priming template, and the polymerase complex remainsbound to the capture oligonucleotide as is shown in (iii).

The structure of the capture complex provided in FIG. 2 is shown indetail in FIG. 3 . In this exemplary illustration, the self-priminghairpin polynucleotide template (300), which is hybridized to a captureoligonucleotide (301), to form a template-capture oligonucleotidecomplex (311). The polynucleotide template (300) comprises a region ofself-complementary double stranded region (302), and a 5′ overhangsequence (303), which comprises a first (304), second (305) and third(306) sequences. First sequence (304) serves as template sequence thatdirects the complementary extension of the 3′ end of the template.Second sequence (305) comprises nucleotides that are complementary tothe nucleotide bases of sequence 307 of the capture oligonucleotide.Third sequence (306) comprises four known nucleotide bases that serve topause polymerase synthesis of the complementary strand. The captureoligonucleotide (301) comprises a first sequence (307), which iscomplementary to the second sequence of the polynucleotide template(305), and to which the capture oligonucleotide hybridizes; and a secondlinker sequence (308), which comprises a purification moiety (310) atits 3′ end. The purification moiety links/tethers the template-captureoligonucleotide complex to a purification moiety (310). As described forFIG. 1 , a polymerase enzyme associates with the double strandedtemplate region (302), and under catalytic conditions, an activepolymerase extends the 3′ end of the template to incorporate nucleotidebases that are complementary to the bases of sequence 304. As the activepolymerase reaches the region of hybridization between the captureoligonucleotide (307) and the template (305), the captureoligonucleotide is displaced from the active polymerase-templatecomplex. An inactive polymerase will not extend the 3′ end of thetemplate, and will fail to displace the capture oligonucleotide. Thepurification moiety is subsequently bound to a solid phase mediumthereby isolating inactive polymerase-template complexes and displacedcapture oligonucleotides from the remaining active-polymerase complexes.

Sequence 306 of the template polynucleotide comprises a stop sequence,which is designed/used to pause the activity of the active polymerase ofthe active polymerase-template complex. A stop sequence can be asequence of four nucleotide bases, wherein the fourth base is differentfrom the first three bases. As the polymerase reaches the stop sequence,only the nucleotide bases that are complementary to the first three ofthe corresponding template bases are provided to pause the activepolymerase. The active-polymerase-template complex is subsequentlyinserted in the membrane of a biochip, where it is reactivated byproviding the nucleotide base that is complementary to the fourth baseof the stop sequence (307), to allow for nanopore sequencing of thetemplate. In some embodiments, the active sequencing complex comprises ananopore the active polymerase is pre-bound to a nanopore, and thenanopore-polymerase-template complex is subsequently inserted into themembrane of the biochip. In other embodiments, the active polymerase isnot prebound to a nanopore, and the polymerase-template complex is boundto a nanopore that is pre-inserted in the membrane of a biochip.

FIG. 4 illustrates an example of the method for preparing activenanopore sequencing complexes. In this example, the polynucleotidetemplate is a continuous polynucleotide template, which is in the formof a dumbbell. The polynucleotide template structure can be linear,continuous e.g. circular, or hairpin. Linear and circular templatesrequire a primer oligonucleotide to prime polymerization of thecomplementary strand, while hairpin templates are self-priming and donot require the primer oligonucleotide. The method includes (i)providing a solution comprising a mixture (400) of polymerase enzyme(401), polynucleotide template (402), oligonucleotide primer (403),capture oligonucleotide (404), and optionally, nanopore (405). Thenanopore, when provided at this step, can be attached to the polymeraseas a nanopore-polymerase complex (406). The polynucleotide templatecomprises a first nucleotide sequence (407) that is complementary tothat of an oligonucleotide primer (403), and a second nucleotidesequence (408) that is complementary to a portion (409) of the sequenceof capture oligonucleotide (404). Optionally, the template includes anucleotide sequence that encodes a stop sequence (409), which haltspolymerization of the complementary strand by the active polymerase. Thecapture oligonucleotide comprises at its 3′ end a purification moiety(410) that enables removal of inactive polymerase-template complexes asdescribed in the following.

In (ii), in the absence of magnesium and dNTPs, i.e. under non-catalyticconditions, a capture complex (411) comprising a polynucleotidetemplate, an oligonucleotide primer, a polymerase enzyme, and a captureoligonucleotide is formed. In some embodiments, the capture complex doesnot include the nanopore.

In (iii), the nanopore sequencing complex is bound to a solid phasemedium (412) to which it is tethered by the capture oligonucleotide.Uncomplexed components i.e. nanopore, polymerase, and nanopore-boundpolymerase are removed, and under catalytic conditions e.g. Mg Cl2 anddNTPs, an active polymerase extends the primer sequence and displacesthe solid-phase bound capture oligonucleotide (413), as shown in (iv).Strand synthesis proceeds until polymerization is halted/paused. In theexemplary process shown in FIG. 4 , polymerization can be paused withEDTA. Alternatively, polymerization can be paused by the stop-sequencecomprised in the polynucleotide template as shown in FIG. 3 . The activenanopore-sequencing complex (414) is subsequently isolated from thesolid-phase bound capture oligonucleotide (413), and is inserted in amembrane e.g. a lipid membrane, of a biochip where nanopore sequencingof the template is performed. In some embodiments, the isolated activepolymerase-complex does not comprise a nanopore, and the isolated activepolymerase complex is bound to a nanopore that is pre-inserted in themembrane of a biochip.

Positive Isolation of Polymerase Complexes and/or Nanopore SequencingComplexes:

In another aspect, a polymerase complex is isolated from its components,by positively isolating the polymerase complex by binding the complex toa solid phase support. In this instance, the polymerase complex is partof the capture complex. An example of a method for positively isolatinga polymerase complex is shown in FIG. 5 .

In a first step (i), polymerase complex components are provided in areaction mixture, and are incubated to allow for their association toform a polymerase complex. In some embodiments, the components in thereaction mixture comprise polynucleotide templates (501) and polymeraseenzyme (502). In other embodiments, the components of the reactionmixture further comprise nanopore proteins (503). In embodiments whereinthe polynucleotide templates are self-priming templates, nooligonucleotide primers are included in the reaction mixture, and apurification moiety is attached to the 5′ end of the templates. Inembodiments, wherein the polynucleotide templates are linear orcircular, oligonucleotide primers (504) are included. Theoligonucleotide primers comprise a purification moiety (505). A solidphase support (506) comprising a purification moiety-binding compoundcan be added at this step, or it can be added in subsequent step (ii).FIG. 5 illustrates the method that uses an oligonucleotide primer as thecapture oligonucleotide.

Subsequently (ii), polymerase complexes (507) are formed by associationof polynucleotide template, oligonucleotide primer comprising apurification moiety, and polymerase enzyme bound to the double strandedtemplate-primer region. In some embodiments, as shown in FIG. 5 , thepolymerase enzyme of the complex is linked to a nanopore protein (503).Association between nanopore and polymerase can occur to form ananopore-polymerase complex (508), which may not be incorporated intothe polymerase complex.

As shown in (iii), the polymerase complex is purified from polymerasecomponents by binding to a solid phase support (506). Theunassociated/unbound components are removed, leaving the polymerasecomplexes bound to the solid phase support, which can be eluted from thesolid phase support to obtain the isolated polymerase complexes (509).Polymerase complexes having a nanopore attached to the polymerase enzymecomponent can be subsequently inserted into a membrane of a biochipwhere sequencing of the template can proceed as described elsewhereherein. Alternatively, polymerase complexes lacking the nanopore can beattached to nanopores that are pre-inserted into the membrane of abiochip.

FIG. 6 illustrates an embodiment of the positive isolation processdescribed in FIG. 5 . In the process shown in FIG. 6 , the solid phasesupport e.g. magnetic beads (501), coated with streptavidin are reactedwith a polynucleotide template having a desthiobiotin purificationmoiety, and a polymerase e.g. DNA polymerase (602). The template that iscomplexed with polymerase enzyme and pore (603), binds to thestreptavidin beads. Unbound polymerase complex components are washedaway (605), and the polymerase complex comprising template, polymeraseand nanopore is eluted (606) from the streptavidin beads to provide apurified nanopore sequencing complex i.e. a pure ternary complex (607).FIG. 6 shows that the solid phase support may be added in the mixture ofpolymerase complex components. Therefore, it is optional that formationof polymerase complexes be allowed to occur prior to adding the solidphase support.

Negative Isolation of Polymerase Complexes and/or Nanopore SequencingComplexes:

In another aspect, a polymerase complex is isolated from its components,by negatively isolating the polymerase complex by binding unassociatedcomplex components to a solid phase support and collecting thepolymerase complex from the unbound fraction of the reaction mixture. Inthis instance, the polymerase components are part of the capturecomplex. An example of a method for negatively isolating a polymerasecomplex is shown in FIG. 7 .

In a first step (i), polymerase complex components are provided in areaction mixture, and are incubated to allow for their association toform a polymerase complex. In some embodiments, the components in thereaction mixture comprise polynucleotide templates (701) and polymeraseenzyme (702). In other embodiments, the components of the reactionmixture further comprise nanopore proteins (703). In embodiments whereinthe polynucleotide templates are self-priming templates e.g. hairpintemplates, no oligonucleotide primers are included in the reactionmixture. In embodiments, wherein the polynucleotide templates are linearor continuous e.g. circular, oligonucleotide primers (704) are included.FIG. 7 illustrates the method that uses an oligonucleotide as thecapture oligonucleotide. The capture oligonucleotide can be aself-priming polynucleotide that associates with polymerase enzymecomponent.

Association of polymerase complex components results in the formation ofa polymerase complex comprising a polynucleotide template and apolymerase enzyme. In the example shown in FIG. 7 (ii), the template iscontinuous, and the polymerase complex further comprises anoligonucleotide primer (705). When present in the reaction mixture,nanopore components can associate with free polymerase components toform free nanopore-polymerase complexes (606). Subsequently, as shown inFIG. 7 (iii), a capture oligonucleotide (707) comprising a purificationmoiety (708) and a solid phase support (709) are added to the reactionmixture. The capture oligonucleotide can be a self-primingpolynucleotide that associates with free polymerase enzyme component,and/or with polymerase-nanopore complex when nanopore is included in thereaction mixture to form capture complexes (710) and (711),respectively. The solid phase support (709) binds the purificationmoiety of the capture complexes providing an unbound fraction that isenriched with polymerase complex (705).

Polymerase complexes comprising a nanopore (713) attached to thepolymerase enzyme can be subsequently inserted into a membrane of abiochip where sequencing of the template can proceed as describedelsewhere herein. Alternatively, polymerase complexes lacking thenanopore can be attached to nanopores that are pre-inserted into themembrane of a biochip.

Purification Moiety and Purification Moiety-Binding Partner/Ligands:

Methods for isolating a polymerase complex from free or unboundpolymerase complex components include affinity chromatography, alsoknown as affinity purification.

In some embodiments, affinity purification is employed in the process ofpositive isolation of the polymerase complex whereby the polymerasecomplex is coupled to a solid support via the binding of a purificationmoiety of the polymerase complex to a purification moiety-bindingpartner on the solid phase support. The free or unbound complexcomponents are washed away, and the solid support-bound polymerasecomplex is subsequently eluted from the solid support to provide apurified polymerase complex fraction. In some embodiments, the bindingof the polymerase complex to the solid phase support is reversible. Theprocess is described with reference to b.

In other embodiments, affinity purification is employed in the processof negative isolation of the polymerase complex components whereby theunwanted, unbound components of a polymerase complex are removed fromthe desired polymerase complex by the binding of a purification moietyof the unbound components to a purification moiety-binding ligand of thesolid phase support. In some embodiments, the binding of the unwanted,unbound polymerase complex components to the solid phase support isreversible. In other embodiments, the binding is irreversible. Theprocess is described, for example, with reference to FIGS. 2, 3, 4, and7 .

In some embodiments, the purification moiety and the purificationmoiety-binding partner are each DNA sequences capable of hybridizing toeach other.

In some embodiments, the purification moiety is biotin and thepurification moiety-binding partner of the solid phase support is avidinor streptavidin. The avidin-biotin system, and in particular thestreptavidin-biotin system, is one of the most widely used affinitybindings in molecular, immunological and cellular assays. In general, atarget molecule that is to be isolated from a mixture is bound eitherdirectly to biotin or to a biotinylated intermediate. Such intermediatemay be almost any molecule or macromolecule that will complex with orconjugate to a target molecule.

In embodiments of the process of positive isolation of the polymerasecomplex, the target molecule that is bound to biotin or to abiotinylated intermediate is the polymerase complex (FIG. 5 ). Inembodiments of the process of displacement purification, active andinactive polymerase complexes are the targets that are bound to biotinor to a biotinylated (FIG. 4 ). In embodiments of the process ofnegative isolation of the polymerase complex, the target molecule thatis bound to biotin or to a biotinylated intermediate is any one of theunbound polymerase components e.g. unbound polymerase enzyme, andunbound polymerase-nanopore complexes (FIG. 7 ). In all embodiments, thebiotinylated target is bound to avidin, streptavidin, or analogs andderivatives thereof, which may be bound to a solid phase for ease ofisolation.

The high affinity of biotin for streptavidin or avidin provides thebasis for many established procedures for the detection and isolation ofbiotin-associated targets. The binding between avidin and biotin(affinity constant, k approx. 10-15 M) is regarded as one of thestrongest non-covalent, biological interactions known. (N. M. Green,Methods Enzymol. 184:51-67, 1990). This strong binding is maintainedeven when either or both binding partners are bound covalently to othermaterials. The bond forms very rapidly and is considered to be stableunder a wide range of pH, temperature and other denaturing conditions(Savage et al., Avidin-Biotin Chemistry: A Handbook, 1992: 1-23,Rockford, Pierce Chemical Company). Dissociation of biotin fromstreptavidin is reported to be about 30 times faster than dissociationof biotin from avidin. (Piran & Riordan. J. Immunol. Methods 133,141-143, 1990).

Some applications which use the biotin-streptavidin (or avidin) linkagerely on the essentially irreversible binding of the two bindingpartners. For example, irreversible binding can be utilized in methodsof negative isolation, whereby the desired polymerase complex is notbound to a solid phase support, and remains isolated in the fractionthat is depleted of unbound polymerase components. In other methodsprovided herein, the isolation of the desired polymerase complexesrelies on the reversible binding of the binding partners, whereby theinteraction between the biotinylated purification moiety and thepurification moiety-binding partner is released by a displacer ligand.For example, reversible binding can be utilized in methods of positiveisolation, whereby the desired polymerase complex is bound to a solidphase support, and is thereby isolated from the unbound polymerasecomplex components.

In some embodiments, releasable binding of the binding partners can beobtained by using modified biotin and derivatives thereof. For example,in some embodiments, the purification binding moiety is dethiobiotin asthe purification moiety, streptavidin as the binding partner, andbiotin, which has a higher affinity constant for streptavidin than doesdethiobiotin, can be used as the displacer ligand. Examples of suitabledisplacer ligands include biotin, dethiobiotin, streptavidin, or avidin.Biotin is a preferred displacer ligand. The sample containing thelinkage, preferably is an aqueous sample, to which the displacer ligandis added, and the reaction mixture allowed to stand under appropriateconditions for a time interval to allow the displacer ligand to bind,and one or both of the components of the linkage may then be separated.Examples of suitable releasable ligands include dethiobiotin,iminobiotin, and functionalized azo dyes, streptavidin, succinylatedavidin, and avidin. Dethiobiotin is preferred. U.S. Pat. No. 5,332,679.Other biotin analogs that can be used as purification binding moietiesinclude biotin sulfone, and biotin derivatives includingcaproylamidobiotin and biocytin U.S. Pat. Nos. 4,656,252; 4,478,914; and4,282,287.

In other embodiments, the purification binding moiety is a derivative ofdesthiobiotin. Modified biotin derivatives are commercially availableunder the name DSB-X™ Biotin (Molecular Probes, Eugene, Oreg., USA).DSB-X™ biotin is a derivative of desthiobiotin, a stable biotinprecursor. DSB-X™ biotin utilizes a seven-atom spacer to increase theability of the DSB-X™ biotin conjugate to bind in the deepbiotin-binding pocket of streptavidin or avidin. The derivative has amoderate affinity for avidin and streptavidin. Their interaction israpidly reversed by low concentrations of free biotin or desthiobiotinat neutral pH and room temperature. Targets complexed with DSB-Xbiotin-labeled molecules can be selectively detected with avidin orstreptavidin conjugates or isolated on affinity matrices followedrelease of DSB-X biotin-labeled biomolecules, under gentle conditions(Hirsch et al. Anal. Biochem. 308, 343-357, 2002). DES-X™ biotin can beconjugated to various molecules, with the use of streptavidin or avidincoated solid phase for immobilization of target, or one may use aDES-X™-coated solid phase and streptavidin or avidin labeled molecules.Molecular Probes provides a variety of antibody conjugates of DSB-X™biotin as well as DSB-X™ biotin agarose.

Releasable streptavidin-biotin or avidin-biotin conjugate can also beobtained, for example, by using chemical cleavable linkers that link thebiotin to the binding partner. Shimkus et al (Proc. Natl. Acad. Sci.USA, 82, pp. 2593-2597, 1985) describe the use of a disulfide bond in alinker that joined biotin to C-5 of the pyrimidine ring, as a means forreversibly binding nucleotides to avidin-agarose columns. This principleis also described in U.S. Pat. No. 4,772,691. In other embodiments,linkages that are specifically cleavable by enzymatic or chemical agentscan be introduced between the biotin molecule and the binding partnere.g. peptide bonds cleavable by various peptidases, disaccharidelinkages cleavable by disaccharidases, or chemical bonds that can beselectively broken under mild reducing, oxidizing, acidic, or basicconditions (U.S. Pat. No. 5,215,927). For example One such linker,Sulfo-NHS-SS-biotin, is commercially available (Pierce BiotechnologyInc, Rockford, Ill. USA). The commercial available CELLection™ BiotinBinder (Dynal Biotech AS, Prod. No. 115.33) contains magnetic beadscoated with streptavidin via a DNA linker to provide for cleavable sitefor target release. The release occurs by incubation with DNAse for 15minutes at room temperature. Photolabile linkages or photocleavablebiotin phosphoramidites (Olejnik et al., Nucleic Acids Res. 24: 361-366,1996) or the use of polymer conjugates together with streptavidinmutants that yields temperature or pH dependent release can also be used(Ding et al., Bioconjugate Chem. 10: 395-400 [1999]; (Bulmus et al.,Bioconjugate Chem. 11:78-83 [2000]). In preferred embodiments, the solidphase comprises magnetic particles and the magnetic particles andattached components or polymerase complexes are isolated from the mixedpopulation of components and complexes by magnetic aggregation.

All parameters involved in the attachment and release system describedherein may vary dependent on targets to be isolated, the ligand systemused, the modified biotin and the avidin or modified avidin, orstreptavidin used, and also the type of solid phase used e.g. size ofthe magnetic beads. All conditions used may readily be determined bythose skilled in the art for any given target and binding pairs used.

In other embodiments, the methods provided herein include the use ofmonomeric avidin (Pierce Biotechnology Inc, Rockford, Ill. USA.),cleavage of the biotin or streptavidin and the use of biotin analogueslike N-hydroxysuccinimide-iminobiotin and amidobiotins.N-hydroxysuccinimide-iminobiotin (NHS-iminobiotin) is a guanido analogof NHS-biotin with a pH sensitive binding affinity for streptavidin.

In some embodiments, the purification moiety-binding partner/ligand isavidin or streptavidin, which can be recombinant or chemically modified,and which can form stable binding to biotin or analogs thereof. Forexample, publication WO 01/05977 by Kulomaa et al. discloses mutationsin both avidin and streptavidin that replace a specific tryptophanresidue with lysine to produce stable dimers that exhibit reversiblebiotin-binding properties. Other modified avidins and streptavidinshaving reduced affinity for biotin and that can be used as purificationmoiety-binding partners in the purification methods provided herein aredescribed for example in U.S. Pat. Nos. 6,022,951, 6,391,571; 6,312,916;6,417,331; 6,165,750 and 6,156,493. Additionally, polypeptides that aresubstantially immunologically equivalent to natural streptavidin and areable to bind to biotin or biotin derivatives or analogues can also beused as purification moiety-binding partners in the methods providedherein (U.S. Pat. No. 5,168,049).

In some embodiments, the ligand i.e. the purifying moiety bindingpartner, is an antibody which is directed against the purifying moiety.The antibody may also be directed against another antibody (that is, ananti-antibody) that is linked to the purification moiety. Bothmonoclonal and polyclonal antibodies can be used, and they can be wholemolecules or various fragments thereof. Antibody specific for aparticular ligand may be produced by methods well known and documentedin the art. Antibodies for use in methods of the present invention maybe of any species, class or subtype providing that such antibodies arecapable of forming a linkage with a particular binding partner and canbe biotinylated with a modified biotin. Thus antibodies for use in thepresent invention include: any of the various classes or sub-classes ofimmunoglobulin, e.g. IgG, IgA, IgM, IgD or IgE derived from any animal,intact antibodies or “fragments” of antibodies, monoclonal orpolyclonal, chimeric antibodies, or synthetically made or alteredantibody-like structures. Also included are functional derivatives or“equivalents” of antibodies e.g. single chain antibodies.

The modified biotin-binding compound (e.g. nitro-streptavidin oravidin), or the modified biotin, if desired, may be covalently attachedto a suitable support through reactive groups on the substrate surfaceby methods well known in the art.

The solid support may be any of the well-known supports or matriceswhich are currently widely used or proposed for immobilization,separation etc., in chemical or biochemical procedures. These may takethe form of particles, sheets, dip-sticks, gels, filters, membranes,microfibre strips, tubes, wells or plates, fibres or capillaries, combs,pipette tips, microarrays or chips or combinations thereof, andconveniently may be made of a polymeric material, e.g. agarose,Sepharose, cellulose, nitrocellulose, alginate, Teflon, latex,acrylamide, nylon membranes, plastic, polystyrene, glass or silica ormetals. Numerous suitable solid supports are commercially available.Preferred solid supports are materials presenting a high surface areafor binding of the modified biotin or modified biotin-binding compound.Such supports will generally have an irregular surface and may forexample be porous or particulate, e.g. particles, fibers, webs, sintersor sieves. Particulate materials e.g. beads are generally preferred dueto their greater binding capacity, particularly polymericbeads/particles.

In some embodiments, a particulate solid support used according to themethods provided herein comprise spherical beads. The size of the beadsis not critical, but they may for example be of the order of diameter ofat least 0.01 μm, and have a maximum diameter of preferably not morethan 10 and more preferably not more than 6 μm. For example, beads ofdiameter 1.0 μm, 2.8 μm and 4.5 μm have been shown to work well.Monodisperse particles, that is those which are substantially uniform insize (e.g. size having a diameter standard deviation of less than 5%)have the advantage that they provide very uniform reproducibility ofreaction. Monodisperse polymer particles produced by the techniquedescribed in U.S. Pat. No. 4,336,173 are also suitable.

Non-magnetic polymer beads suitable for use in the method of theinvention are available from Dynal Biotech AS (Oslo, Norway) under thetrademark DYNOSPHERES, as well as from Qiagen, GE Healthcare LifeSciences, Serotec, Seradyne, Merck, Nippon Paint, Chemagen, Promega,Prolabo, Polysciences, Agowa and Bangs Laboratories.

However, to aid manipulation and separation of immobilized material, andalso to facilitate automation if required, magnetizable (“magnetic”)beads are preferred. The term “magnetic” as used herein means that thesupport is capable of having a magnetic moment imparted to it whenplaced in a magnetic field, and thus is displaceable under the action ofthat field. In other words, a support comprising magnetic particles mayreadily be removed from other components of a sample by magneticaggregation, which provides a quick, simple and efficient way ofseparating the particles following the binding of any modified biotin ormodified biotinylated moieties.

Thus, the magnetic particles with the modified biotin or modifiedbiotinylated moieties attached via conjugation to a modifiedbiotin-binding compound, e.g. nitro-streptavidin (avidin), may beremoved onto a suitable surface by application of a magnetic field, e.g.using a permanent magnet. It is usually sufficient to apply a magnet tothe side of the vessel containing the sample mixture to aggregate theparticles to the wall of the vessel and to remove the remainder of thesample so that the remaining sample and/or the particles are availablefor any desired further steps. The well-known monodisperse polymericsuperparamagnetic beads sold by Dynal Biotech AS (Oslo, Norway) underthe trade mark DYNABEADS, are exemplary of commercially availablemagnetic particles which may be used or modified for use according tothe invention.

Enzymes of Enzyme-Polymer Complexes and Enzyme-Nanopore Complexes:

The enzymes of the polymerase complexes and of the nanopore sequencingcomplexes include polynucleotide processing enzymes, e.g. DNA and RNApolymerases, and reverse transcriptases. The enzyme of the polymerasecomplexes and of the nanopore sequencing complexes can be a wild-typeenzyme, or it can be a variant form of the wild-type enzyme. Variantenzymes can be engineered to possess characteristics that are alteredrelative to those of the parent enzyme. In some embodiments, the enzymeof the enzyme-polymer complex that is altered is a polymerase. Thealtered characteristics of the polymerase enzyme include changes inenzyme activity, fidelity, processivity, elongation rate, stability, orsolubility. The polymerase can be mutated to reduce the rate at whichthe polymerase incorporates a nucleotide into a nucleic acid strand(e.g., a growing nucleic acid strand). The reduced velocities (andimproved sensitivities) can be achieved by a combination ofsite-specific mutagenesis of the nanopore protein and the incorporationof DNA processing enzymes e.g. DNA polymerase, into the nanopore.

Examples of DNA polymerase enzymes that can be complexed with templatesubstrates in polymerase complexes and/or nanopore sequencing complexesinclude without limitation wild type or variants of Pol6 DNA polymerasefrom Clostridium phage phiCPV4 (GenBank Accession No.: AFH27113.1, andthe Bacillus subtilis bacteriophage DNA polymerase Phi29 (GenbankAccession No. X53371). The wild type and variant polymerase preferablydisplay at least one of the altered characteristics disclosed herein.

In some cases, the rate at which a nucleotide is incorporated into anucleic acid strand can be reduced by functionalizing the nucleotideand/or template strand to provide steric hindrance, such as, forexample, through methylation of the template nucleic acid strand. Insome instances, the rate is reduced by incorporating methylatednucleotides.

The enzymes of the polymerase complexes and of the nanopore sequencingcomplexes may be modified to comprise one or more attachment componentsand/or attachment sites that serve to link the enzyme of the polymerasecomplex to the nanopore that is inserted into the membrane of a biochip.Alternatively, enzymes of the polymerase complexes and of the nanoporesequencing complexes may be modified to comprise one or more attachmentcomponents and/or attachment sites that serve to link the enzyme of thepolymerase complex to a nanopore to form a nanopore sequencing complexthat is inserted into the membrane of a biochip. Similarly, the nanoporeof the polymerase complex and/or of the nanopores sequencing complex mayalso be modified to comprise one or more attachment components and/orattachment sites to link the nanopore to the enzyme-polymer complex.

Nanopores:

The nanopores of the nanopore sequencing complex include withoutlimitation biological nanopores, solid state nanopores, and hybridbiological-solid state nanopores. Biological nanopores of the nanoporesequencing complexes include OmpG from E. coli, sp., Salmonella sp.,Shigella sp., and Pseudomonas sp., and alpha hemolysin from S. aureussp., MspA from M. smegmatis sp. The nanopores may be wild-typenanopores, variant nanopores, or modified variant nanopores.

Variant nanopores can be engineered to possess characteristics that arealtered relative to those of the parent enzyme. In some embodiments, thevariant nanopore of the nanopore sequencing complex is engineered toreduce the ionic current noise of the parental nanopore from which it isderived. An example of a variant nanopore having an alteredcharacteristic is the OmpG nanopore having one or more mutations at theconstriction site, which decrease the ionic noise level relative to thatof the parent OmpG. The reduced ionic current noise provides for the useof these OmpG nanopore variants in single molecule sensing ofpolynucleotides and proteins. In other embodiments, the variant OmpGpolypeptide can be further mutated to bind molecular adapters, whichwhile resident in the pore slow the movement of analytes, e.g.,nucleotide bases, through the pore and consequently improve the accuracyof the identification of the analyte (Astier et al., J Am Chem Soc10.1021/ja057123+, published online on Dec. 30, 2005).

Modified variant nanopores are typically multimeric nanopores whosesubunits have been engineered to affect inter-subunit interaction.Altered subunit interactions can be exploited to specify the sequenceand order with which monomers oligomerize to form the multimericnanopore in a lipid bilayer. This technique provides control of thestoichiometry of the subunits that form the nanopore. An example of amultimeric nanopore whose subunits can be modified to determine thesequence of interaction of subunits during oligomerization is an aHLnanopore.

Linking Nanopore to Polymerase:

The polymerase complex e.g. polymerase-polynucleotide complex, can beattached to the nanopore in any suitable way. Attaching polymerasecomplexes to nanopores may be achieved using the SpyTag/SpyCatcherpeptide system (Zakeri et al. PNAS109:E690-E697 [2012]) native chemicalligation (Thapa et al., Molecules 19:14461-14483 [2014]), sortasesystem_(Wu and Guo, J Carbohydr Chem 31:48-66 [2012]; Heck et al., ApplMicrobiol Biotechnol 97:461-475 [2013]), transglutaminase systems(Dennler et al., Bioconjug Chem 25:569-578 [2014]), formylglycinelinkage (Rashidian et al., Bioconjug Chem 24:1277-1294 [2013]), or otherchemical ligation techniques known in the art.

In some instances, the polymerase is linked to the nanopore usingSolulink™ chemistry. Solulink™ can be a reaction between HyNic(6-hydrazino-nicotinic acid, an aromatic hydrazine) and 4FB(4-formylbenzoate, an aromatic aldehyde). In some instances, thepolymerase is linked to the nanopore using Click chemistry (availablefrom LifeTechnologies, for example).

In some cases, zinc finger mutations are introduced into a nanopore e.g.an a-hemolysin molecule and then a molecule is used (e.g., a DNAintermediate molecule) to link the polymerase to the zinc finger siteson the hemolysin.

Additionally, polymerase complexes can be attached to a nanopore e.g.aHL, OmpG, by means of a linker molecule that is attached to a nanoporeat an attachment site. In some cases, the polymerase-DNA complex isattached to the nanopore with molecular staples. In some instances,molecular staples comprise three amino acid sequences (denoted linkersA, B and C). Linker A can extend from a nanopore monomer, Linker B canextend from the polymerase of the polymerase-DNA complex, and Linker Cthen can bind Linkers A and B (e.g., by wrapping around both Linkers Aand B) and thus the polymerase of the polymerase-DNA complex to thenanopore. Linker C can also be constructed to be part of Linker A orLinker B, thus reducing the number of linker molecules.

Other linkers that may find use in attaching the polymerase to ananopore are direct genetic linkage (e.g., (GGGGS)₁₋₃ amino acid linker(SEQ ID NO: 1)), transglutaminase mediated linking (e.g., RSKLG (SEQ IDNO: 2)), sortase mediated linking, and chemical linking through cysteinemodifications. Specific linkers contemplated as useful herein are(GGGGS)₁₋₃ (SEQ ID NO: 1), K-tag (RSKLG (SEQ ID NO: 2)) on N-terminus,ΔTEV site (12-25), ΔTEV site+N-terminus of SpyCatcher (12-49).

An exemplary method for attaching a polymerase complex to a nanopore ina membrane involves attaching a linker molecule to a nanopore ormutating a nanopore to have an attachment site and then attaching apolymerase-polynucleotide complex to the attachment site or attachmentlinker. The polymerase-polynucleotide complex is attached to theattachment site or attachment linker after the nanopore is inserted inthe membrane. In some cases, a polymerase-polynucleotide complex isattached to each of a plurality of nanopores that are inserted into amembrane and disposed over wells and/or electrodes of a biochip.

In some instances, the enzyme of the enzyme-polymer complex is expressedas a fusion protein that comprises a linker peptide. In someembodiments, a polymerase is the enzyme of the enzyme-polymer complex,and a polynucleotide is the polymer. The polymerase of thepolymerase-polynucleotide complex is expressed as a fusion protein thatcomprises a SpyCatcher polypeptide, which can be covalently bound to ananopore that comprises a SpyTag peptide (Zakeri et al. PNAS109:E690-E697 [2012]).

Polymerase complexes may be attached to nanopores using methodsdescribed, for example, in PCT/US2013/068967 (published asWO2014/074727; Genia Technologies, Inc.), PCT/US2005/009702 (publishedas WO2006/028508; President and Fellows of Harvard College), andPCT/US2011/065640 (published as WO2012/083249; Columbia University).

Stoichiometries:

The enzymes of the polymerase complex e.g. a DNA polymerase, may bemodified to comprise one or more attachment components and/or attachmentsites that serve to link the enzyme-polymer complex to the nanoporeinserted into the membrane. Similarly, the nanopore to which thepolymerase complex is attached may also be modified to comprise one ormore attachment components and/or attachment sites to link the nanoporeto the polymerase complex.

In some embodiments, a single polymerase complex is attached to thenanopore in the membrane. In other embodiments, two or more polymerasecomplexes are attached to the nanopore in the membrane. The singlepolymerase complex may be attached to the nanopore at one or moreattachment sites present on the nanopore protein. In some embodiments,one or more polymerase complexes are attached to a monomeric nanoporeprotein e.g. an OmpG nanopore. In other embodiments, one or morepolymerase complexes are attached to a multimeric nanopore protein thatcomprises at least two nanopore subunits e.g. heptameric aHL nanopore. Apolymerase complex can be attached to an attachment site on a singlesubunit of a multimeric nanopore. Alternatively, the polymerase complexmay be attached to the multimeric nanopore at two or more attachmentssites present on each of two or more subunits of a multimeric nanopore.

Polymerase complexes may be attached to one or more subunits ofhomo-oligomeric or of hetero-oligomeric nanopores. For example, apolymerase complex may be coupled to an aHL nanopore consisting of 7identical subunits, which may be wild-type, variants, or modifiedvariants. Alternatively, the polymerase complex may be coupled to an aHLnanopore consisting of at least two different subunits, of which one ormore may be modified.

Oligomeric nanopores e.g. a-HL, are proteins that can self-assemble fromsubunits that are monomers, concatemers of monomers, or a combination ofmonomers and concatemers of monomers. Subunits that are concatemers ofmonomers can comprise two, three or more monomers that are linked toeach other by a linker or that are each encoded by a singlepolynucleotide as a fusion protein. Accordingly, the polymerase complexmay be attached to a monomer subunit, or to a concatemer of monomersubunits of an oligomeric nanopore. In some embodiments, the polymerasecomplex is a DNA polymerase-DNA template complex that is attached to amonomeric nanopore e.g. an OmpG, which may be wild type, or a varianthaving altered characteristics. In other embodiments, the polymerasecomplex is a DNA polymerase-DNA template complex that is attached to anoligomeric nanopore, which can be a homo-oligomeric or ahetero-oligomeric nanopore e.g. an aHL nanopore, which may be wild-type,a variant, or a modified variant nanopore.

Forming Bilayers on Biochips:

Methods for creating lipid bilayers comprising nanopores in a biochipare described at least at paragraphs [00131]-[00196] inPCT/US2014/061854 (published as WO2015/061511, Genia Technologies,Inc.). A lipid bilayer can be created on top of each one of multipleelectrodes that make up an array of individually controlled electrodesand a single nanopore can be inserted into each bilayer atop eachelectrode in an array of individually controlled electrodes.

In some embodiments, sequencing nanopore complexes are formed on asemiconductor chip having multiple electrodes, to which a lipid solutionis applied to create a lipid bilayer. The lipid solution may be asolution of an organic solvent e.g. decane, hexane, tridecane etc., andlipid molecules, such as diphytanoylphosphatidylcholine (DPhPC),1,2-diphytanoyl-sn-glycero-3-phosphocholine, Lysophosphatidylcholine(LPC), 1,2-Di-O-Phytanyl-sn-Glycero-3-phosphocholine (DoPhPC),palmitoyl-oleoyl-phosphatidyl-choline (POPC),dioleoyl-phosphatidyl-methylester (DOPME),dipalmitoylphosphatidylcholine (DPPC), phosphatidylcholine,phosphatidylethanolamine, phosphatidylserine, phosphatidic acid,phosphatidylinositol, phosphatidylglycerol, sphingomyelin,1,2-di-O-phytanyl-sn-glycerol;1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethyleneglycol)-350];1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethyleneglycol)-550];1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethyleneglycol)-750];1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethyleneglycol)-1000];1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethyleneglycol)-2000]; 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-lactosyl;GM1 Ganglioside, or any combination thereof. Methods for applying thelipid solution and forming the lipid bilayer is described at least atparagraphs [00148] to [00152] of WO2015/061510.

Inserting a Nanopore:

In some instances, a nanopore is inserted in the membrane (e.g., byelectroporation). Methods for inserting a nanopore in a membrane areprovided at least at paragraphs [00197]-[00203] of WO2015/061510. Thenanopore can be inserted by a stimulus signal such as electricalstimulus, pressure stimulus, liquid flow stimulus, gas bubble stimulus,sonication, sound, vibration, or any combination thereof.

In some embodiments, inserting the nanopore comprises applying astimulus (e.g., electroporation pulse) through the electrode(s) tofacilitate the insertion of said nanopore. In some cases, this isfollowed by a second electrical detection pulse to detect the insertionof said nanopore in said lipid bilayer. In some cases, the applicationof a stimulus voltage and subsequent detection voltage is repeated withthe stimulus voltage gradually increasing in magnitude until a pore isdetected during a detection pulse. The electrode is then disabled and nofurther pulses are applied. In other embodiments, the nanopore insertsitself into the membrane.

Nanopores of the nanopore sequencing complexes described herein may beinserted in a membrane, e.g. a lipid bilayer, and disposed adjacent orin proximity to a sensing electrode of a sensing circuit, such as anintegrated circuit of a nanopore based sensor e.g. a biochip. Thenanopore may be inserted in a membrane and disposed of a well and/orsensing electrodes in the biochip. Multiple nanopore sensors may beprovided as arrays. Biochips and methods for making biochips aredescribed in PCT/US2014/061854 (published as WO2015/061511, GeniaTechnologies, Inc.), which is herein incorporated by reference in itsentirety.

Methods for Sequencing:

The molecules being characterized using the nanopores of the nanoporesequencing complexes described herein can be of various types, includingcharged or polar molecules such as charged or polar polymeric molecules.Specific examples include ribonucleic acid (RNA) and deoxyribonucleicacid (DNA) molecules. The DNA can be a single-strand DNA (ssDNA) or adouble-strand DNA (dsDNA) molecule.

In one aspect, provided are methods for sequencing nucleic acids usingthe nanopore sequencing complexes described herein. In some embodiments,the methods comprise isolating a polymerase complex from a mixture ofpolymerase complex components according to any one of the methodsdescribed herein, and attaching the isolated polymerase complex to ananopore inserted in a lipid membrane of a biochip. In otherembodiments, the sequencing methods comprise isolating a nanoporesequencing complex from a mixture of complex components, and insertingthe isolated nanopore sequencing complex into a lipid membrane of abiochip. The nanopore sequencing complexes prepared as described hereincan be used for determining the sequence of nucleic acids according toother nanopore sequencing platforms known in the art that utilizeenzymes in the sequencing of polynucleotides. For example, nanoporesequencing complexes can be prepared according to the method describedherein for sequencing nucleic acids according to the helicase andexonuclease-based methods of Oxford Nanopore (Oxford, UK), Illumina (SanDiego, Calif.), and the nanopore sequencing-by-expansion of StratosGenomics (Seattle, Wash.).

In some embodiments, sequencing of nucleic acids comprises preparingnanopore sequencing complexes as described herein, and determiningpolynucleotide sequences using tagged nucleotides as is described inPCT/US2013/068967 (entitled “Nucleic Acid Sequencing Using Tags” filedon Nov. 7, 2013, which is herein incorporated by reference in itsentirety). For example, a nanopore sequencing complex that is situatedin a membrane (e.g., a lipid bilayer) adjacent to or in sensingproximity to one or more sensing electrodes, can detect theincorporation of a tagged nucleotide by a polymerase as the nucleotidebase is incorporated into a strand that is complementary to that of thepolynucleotide associated with the polymerase, and the tag of thenucleotide is detected by the nanopore. The polymerase-polynucleotidecomplex can be associated with the nanopore as described above.

Tags of the tagged nucleotides can include chemical groups or moleculesthat are capable of being detected by a nanopore. Examples of tags usedto provide tagged nucleotides are described at least at paragraphs[0414] to [0452] of PCT/US2013/068967. Nucleotides may be incorporatedfrom a mixture of different nucleotides, e.g., a mixture of tagged dNTPswhere N is adenosine (A), cytidine (C), thymidine (T), guanosine (G) oruracil (U). Alternatively, nucleotides can be incorporated fromalternating solutions of individual tagged dNTPs, i.e., tagged dATPfollowed by tagged dCTP, followed by tagged dGTP, etc. Determination ofa polynucleotide sequence can occur as the nanopore detects the tags asthey flow through or are adjacent to the nanopore, as the tags reside inthe nanopore and/or as the tags are presented to the nanopore. The tagof each tagged nucleotide can be coupled to the nucleotide base at anyposition including, but not limited to a phosphate (e.g., gammaphosphate), sugar or nitrogenous base moiety of the nucleotide. In somecases, tags are detected while tags are associated with a polymeraseduring the incorporation of nucleotide tags. The tag may continue to bedetected until the tag translocates through the nanopore afternucleotide incorporation and subsequent cleavage and/or release of thetag. In some cases, nucleotide incorporation events release tags fromthe tagged nucleotides, and the tags pass through a nanopore and aredetected. The tag can be released by the polymerase, or cleaved/releasedin any suitable manner including without limitation cleavage by anenzyme located near the polymerase. In this way, the incorporated basemay be identified (i.e., A, C, G, T or U) because a unique tag isreleased from each type of nucleotide (i.e., adenine, cytosine, guanine,thymine or uracil). In some situations, nucleotide incorporation eventsdo not release tags. In such a case, a tag coupled to an incorporatednucleotide is detected with the aid of a nanopore. In some examples, thetag can move through or in proximity to the nanopore and be detectedwith the aid of the nanopore.

In some cases, tagged nucleotides that are not incorporated pass throughthe nanopore. The method can distinguish between tags associated withun-incorporated nucleotides and tags associated with incorporatednucleotides based on the length of time the tagged nucleotide isdetected by the nanopore. In one embodiment, an un-incorporatednucleotide is detected by the nanopore for less than about 1 millisecondand an incorporated nucleotide is detected by the nanopore for at leastabout 1 millisecond.

Thus, in one aspect, the disclosure provides for a method for sequencinga polynucleotide from a biological sample, with the aid of a nanoporesequencing complex. The sample polynucleotide is combined with apolymerase, to provide the enzyme-polymer complex portion of thenanopore sequencing complex. In one embodiment, the samplepolynucleotide is a sample ssDNA strand, which is combined with a DNApolymerase to provide a DNA polymerase-DNA complex. The DNApolymerase-sample ssDNA strand is subsequently attached to a nanoporethat has been inserted into a membrane e.g. a lipid bilayer, to providethe nanopore sequencing complex. The nanopore portion of the sequencingcomplex is positioned in the membrane adjacent to or in proximity of asensing electrode, as described elsewhere herein. The resulting nanoporesequencing complex is capable of determining the sequence of nucleotidebases of the sample DNA as described elsewhere herein. In otherembodiments, the nanopore sequencing complex determines the sequence ofdouble stranded DNA. In yet other embodiments, nanopore sequencingcomplex determines the sequence of RNA.

In one embodiment, the method provides for sequencing a samplepolynucleotide with the aid of a nanopore sequencing complex adjacent toa sensing electrode, and comprises (a) preparing a nanopore sequencingcomplex by isolating a polymerase complex and attaching the polymerasecomplex to a nanopore inserted in a lipid membrane of a biochip.Alternatively, the method comprises isolating a nanopore sequencingcomplex from a mixture of complex components, and inserting the nanoporesequencing complex in the lipid membrane of a biochip. The methodfurther comprises (b) providing tagged nucleotides into a reactionchamber comprising the nanopore sequencing complex, wherein anindividual tagged nucleotide of the tagged nucleotides contains a tagcoupled to a nucleotide, which tag is detectable with the aid of thenanopore; (c) carrying out a polymerization reaction, with the aid ofthe polymerase, thereby incorporating an individual tagged nucleotide ofthe tagged nucleotides into a growing strand complementary to the singlestranded nucleic acid molecule from the nucleic acid sample; and (d)detecting, with the aid of the nanopore, a tag associated with theindividual tagged nucleotide during and/or upon incorporation of theindividual tagged nucleotide, wherein the tag is detected with the aidof the nanopore when the nucleotide is associated with the polymerase.Other embodiments of the sequencing method that comprise the use oftagged nucleotides with the present nanopore sequencing complexes forsequencing polynucleotides are provided in WO2014/074727, which isincorporated herein by reference in its entirety.

Sequencing nucleic acids using AC waveforms and tagged nucleotides isdescribed in US Patent Publication US2014/0134616 entitled “Nucleic AcidSequencing Using Tags”, filed on Nov. 6, 2013, which is hereinincorporated by reference in its entirety. In addition to the taggednucleotides described in US2014/0134616, sequencing can be performedusing nucleotide analogs that lack a sugar or acyclic moiety, e.g.,(S)-Glycerol nucleoside triphosphates (gNTPs) of the five commonnucleobases: adenine, cytosine, guanine, uracil, and thymidine (Horhotaet al. Organic Letters, 8:5345-5347 [2006]).

Nucleic Acid Adaptor for Isolating Active Polymerase Complexes:

As mentioned above, also disclosed is a nucleic acid adaptor forisolating active polymerase complexes, polymerase complexes comprisingthe nucleic acid adaptor, and methods for isolating active polymerasecomplexes using the nucleic acid adaptor. The isolated polymerasecomplexes are subsequently incorporated into membranes of biochips toenable nanopore sequencing of polynucleotides.

Aspects discussed herein above with respect to other methods andembodiments of the present disclosure are also applicable with regard tothe nucleic acid adaptor for isolating active polymerase complexes, thepolymerase complexes comprising the nucleic acid adaptor, the methodsfor isolating active polymerase complexes using the nucleic acidadaptor, and other methods discussed herein that are enabled by the useof the nucleic acid adaptor. Therefore, such aspects are not beingrestated in this section, but one of ordinary skill in the art canreadily understand that such previously discussed aspects andembodiments can relate to the nucleic acid adaptor and its relatedmethods.

Active Fraction Enrichment Via Biotin Labeling and Streptavidin BeadCapture:

Provided below is a description of various aspects of an embodiment ofthe nucleic acid adaptor of the present disclosure, particularly as itpertains to active fraction enrichment via biotin labeling andstreptavidin bead capture.

In one embodiment, the adaptor contains a runway section (sequence)composed of 3 of the 4 nucleotides. This runway section can be 2 to 50bases long, preferably 8 to 12 bases.

In a more particular embodiment of the adaptor, one of the runway basesmay be present 4 to 6 times or a large percentage of the bases.Conversely, one of the bases in the runway could be very sparse (e.g., 1to 2 bases).

The adaptor and runway sequence are ligated to sample DNA or RNA andform part of the pore/polymerase/sample DNA or polymerase/DNA complex.

To enrich for functional (active) polymerase complexes, a mixture ofappropriate buffer, salt, nucleotides (i.e., 3 of 4 nucleotide basesthat are complementary to the 3 of 4 nucleotides of the runwaysequence), and required divalent metal for enzymatic activity is used toenable the extension of new nucleotide strands comprising the 3 of 4nucleotide bases complementary to the 3 of 4 nucleotides of the runwaysequence. One or more of the 3 nucleotides in the mixture can have acapture moiety attached to the base or position on the base that willnot interfere with this biotin. The capture moiety can be any moleculewith an affinity for another molecule. As indicated above, the adaptorincludes a stop region after the runway sequence. The stop regioncomprises the nucleotide base (e.g., cytosine) that is not included asone of the three nucleotide bases (e.g., thymine, guanine, adenine)making up the runway sequence and that is not complementary to any ofthe 3 of 4 nucleotide bases in the mixture. Once the active polymerasereaches the end of the runway sequence, it then encounters the stopregion, at which point the polymerase must stop because of a lack of anappropriate nucleotide needed for extend the strand.

The active enzyme ternary complexes extend a new copy strand andincorporate the biotin labeled nucleotides. When the enzyme reaches theposition on the runway where no matching nucleotides are present in themix, it stops. The ternary complex or polymerase/DNA has been labeled.

The biotin labeled complexes represent those complexes that have anactive polymerase. Non-active polymerase complexes are not labeled.

A bead or solid surface support functionalized or attached to a moleculeor molecules that have an affinity for the labeling moiety are added tothe mix and labeled molecules are attracted and caught by the bead/solidsupport. Unlabeled, inactive complex is washed away and the remaining,active complex is eluted from the bead/solid support and run on thechip. Alternately, the active complex can stay attached to the bead orsolid support and then run on the chip.

The result is the sample complex mix; pore/polymerase/templateDNA/primer or polymerase/template/primer has been enriched for activepolymerase versions of the above complexes.

The schematic shown in FIG. 15 illustrates one embodiment of a nucleicacid adaptor provided herein for isolating active polymerase complexes.As illustrated, the adaptor is ligated to a sample DNA. The adaptor isalso shown to have primer annealed to the primer recognition sequence ofthe adaptor and a polymerase enzyme associated with the adaptor prior toprimer extension. As illustrated, the runway sequence is 12 nucleotidebases in length and includes only adenine (A), guanine (G), and thymine(T) nucleotide bases, while the stop region includes only two cytosine(C) nucleotide bases.

The schematic shown in FIG. 16 illustrates the same nucleic acid adaptoras shown in FIG. 15 . However, as illustrated in FIG. 16 , the adaptoris also shown to have a primer annealed to the primer recognitionsequence of the adaptor and an extended sequence complementary to therunway sequence. The extended sequence is 12 nucleotide bases in lengthand includes only adenine (A), cytosine (C), and thymine (T) nucleotidebases. Also shown is a polymerase enzyme associated with the adaptor.Further, the cytosine (C) nucleotide bases of the extended sequence alsoincludes biotin or desthio-biotin moieties.

Below is an example of the reagent mixture added to promote extension ofthe primer using the adaptor having the runway sequence shown in FIGS.15 and 16 , as follows:

Reagent Mixture:

Reagent dTTP mix added dATP to biotin - dCTP or desthio-biotin-dCTPpromote {open oversize bracket} MgCl₂ or other catalyitic metalextension HEPES buffer Low [ ] of salt (monovalent salt)

-   -   Mix is missing dGTP so that extension of nucleic acid strand        will stop at C position on adaptor    -   The mix may contain some proportion of non-biotinylated or        non-desthiobiotinylated dCTP so that not every “G” position on        the template is covered with labeled dCTP.    -   It is also noted that labeled nucleotides can be removed/washed        away from the active template complex while the complex is        associated with the solid phase, prior to adding the 4th        nucleotide during sequencing.

This method is simple and by optimizing bead binding capacity andlabeled dCTP and template concentrations effective enrichment andapplication to the chip or membrane can be attained.

Once the enriched complex is loaded to the chip andpore/polymerase/template DNA/primer complex is set up over theelectrode/wells, the remaining complex and reagents are washed from thechip and replaced with a full set of nucleotide tags and the necessaryreagents to perform sequencing by synthesis with Genia nucleotide tags.

Analysis of the resulting sequence is made easier as an anticipatedstart site at the stop bases can be predicted.

When the polymerase has extended complementary sequence around theentire circular template it will return to the primer and displace it asit continues synthesis. The biotin or desthio-biotin labeled bases arealso displaced and are not part of the 2nd or subsequent passes aroundthe template DNA or RNA.

The biotin or desthio-biotin labeling/enrichment can also be performedon linear templates.

The schematic shown in FIG. 17 illustrates one embodiment of a nucleicacid adaptor provided herein for isolating active polymerase complexes.As illustrated, the adaptor is ligated to a sample DNA. The adaptor islinear and is also shown to have primer annealed to the primerrecognition sequence of the adaptor. Embodiment (1) illustrates theadaptor before enrichment extension of the runway sequence. Embodiment(2) illustrates the adaptor after enrichment extension of the runwaysequence. Those linear samples with no extended product on the runwaywill not be labeled and subsequently will be washed away in enrichment.

EXAMPLES Example 1

Displacement Purification—Isolation of Active Polymerase Complexes

This example relates to a method for purifying an activepolymerase-template complex. The active complex comprises an activepolymerase, which is associated with a self-primed DNA template. Acircular DNA can also be used in the presence of an oligonucleotideprimer that can be extended in subsequent nanopore sequencing of thetemplate.

According to the method, the active complex was purified from inactivecomplexes by virtue of the activity of the polymerase as describedelsewhere herein.

Ternary complexes were prepared by incubating self-priming DNAtemplates, polymerase, and biotinylated capture oligonucleotides in afirst reaction mixture (1). In cases where a circular DNA template isused, a primer oligonucleotide is included as a component of the ternarycomplex. Monomeric avidin magnetic beads (BcMag™ from Bioclone Inc. SanDiego, Calif.) were prepared according to the manufacturer'sinstructions by treating the beads with 1 mg/ml BSA, then removingexcess BSA by washing the beads with wash buffer 75 mM KGlu, 20 mMHEPES, 3 mM CaCl₂, 1 mM TCEP, 0.01% tween 20, pH 8.0. Details forconditioning the avidin beads are provided by the manufacturer atwww.bioclone.us/files/BcMag_Monomer_Avidin_Magnetic_Beads.pdf.

Two hundred microliters of reaction mixture (1) comprising ternarycomplexes were incubated with the prepared beads for 30 minutes at roomtemperature. The reaction mixture (1) was placed on a magneticseparator, and the supernatant containing unbound complex components wasremoved.

The ternary complexes bound to the beads were washed then resuspendedwith extension buffer 75 mM KGlu, 20 mM HEPES, 10 mM MgCl2, 150 uM dNTP,1 mM TCEP, 0.01% tween20, pH 8.0 for 5 minutes at room temperature toallow for extension of the self-primed template. The beads were placedon a magnetic separator, and the supernatant was collected, as complexescomprising active polymerase would be dissociated from the captureoligonucleotide.

Purification of the active polymerase complex was visualized using aurea-TBE gel stained with SYBR gold stain (FIG. 8 ). Lane 1 shows themolecular weight markers. Lane 2 shows the self-priming template coupledwith biotinylated capture oligonucleotide. Lane 3 shows the biotinylatedcapture oligonucleotide alone. Lane 7 shows the unbound fraction. Lane 8shows the fraction following the first wash of the beads. Lane 9 showsthe fraction containing the purified active polymerase complex havingthe extended DNA template containing the active polymerase complex. Lane10 shows the fraction from the second wash. Lanes 11 and 12 show thatunextended DNA templates complexed with the biotinylated oligonucleotideremained bound to the avidin beads. Lane 12 shows that in thisexperiment, some of the active polymerase and associated extended DNAtemplate had not been eluted from the beads.

These data show that active polymerase complexes can be isolatedaccording to the displacement purification method described herein.

Example 2

Positive Enrichment—Isolation of Polymerase Complexes

This example relates to a method for purifying a sequencing complexcomprising a nanopore attached to a polymerase, which in turn isassociated to a polynucleotide template. In the positive enrichmentmethod the affinity purification is of activenanopore-polymerase-template complexes.

A schematic of the process is provided in FIGS. 5 and 6 .

Briefly, self-priming hairpin DNA template was annealed to adesthiobiotinylated (DES) primer having a TEG linker according to themanufacturer's instructions. The DES primer was conditioned by dilutingit from stock to 50 uM with PacBio Elution Buffer (catalog no.100-159-800), then incubating it at 80 C, then cooling it to 4 C. Theconditioned primer was annealed to template DNA at 20 C for 30 minutes,then cooled to 4 C for immediate use or to −20 C for storage.Biotinylated template was incubated on ice for 1 hour with 0.1 uM Pol2polymerase in 80 ul of Flow Comp Flexi beads (Life Tech). 0.1 uM aHLnanopore protein was added to the template polymerase mixture, andallowed to incubate for 40 minutes. The reaction tube was placed on amagnetic separator, and the supernatant was removed and discarded. Thebeads were washed with 75 mM KGlu, 0.01% Tween20, 20 mM HEPES, 3 mMSrCL2, and 5 mM TCEP. The bead-bound ternary complex was eluted from thebeads in 500 mM KGlu, 20 mM HEPES, 2 mM Biotin, 20 mM HEPES, 1 mM SrCL2,0.0001% Tween20, and 6 mM blocked nucleotides. The supernatant wascollected, and the beads were washed again in release buffer to collectresidual ternary complex. (W1) and elution fractions (E1 and E2) werevisualized by SDS-PAGE (see FIG. 9 ).

The polymerase activity of the fraction enriched with ternary complexwas assayed for its ability to extend the template in the presence ofdNTPs, and the extension product was visualized by urea-SDS-PAGE (seeFIG. 10 ). The polymerase activity obtained by the positive enrichmentmethod was compared polymerase activity of polymerase complexes obtainedby a standard method that uses a mixture of template, polymerase, andnanopore to form polymerase complexes (Eintof), but that does notcomprise enriching fractions by isolating the polymerase complexes fromthe unbound components. The results are shown in FIG. 10 , which showsthat the product of polymerase extension was visible in fractions thathad been enriched using the avidin beads according to the positiveenrichment. Extension product was not visualized in the mixtureresulting from use of the unenriched method (Eintof).

The experiment was repeated using adaptor dimers to provide dumbbellshaped DNA template. A schematic of the process is provided in FIG. 5 .

In this instance, an oligonucleotide primer was labeled withdesthiobiotin, and incubated with template, polymerase and nanopore.Monomeric streptavidin beads were used for the purification. Theenrichment protocol used DNA adaptor dimers as template, Pol2polymerase, and aHL nanopore in equimolar ratios of 0.1:0.1:0.1. Thecomponents were allowed to react for 1.5 hours at 4 C. Two preparationsof unenriched mixtures (Eintof) were used as controls. The firstunenriched mixture comprised adaptor dimer DNA template, Pol2polymerase, and aHL in equimolar ratios of 0.4:0.2:0.1; the secondunenriched mixture comprised a linear DNA template JAM1A (99 bases),Pol2 polymerase, and aHL nanopore in equimolar ratios of 0.4:0.2:0.1.The components of the unenriched mixtures were incubated overnight at 4C. The enriched fractions comprising the ternary complexes obtained bythe positive enrichment method were applied onto the membrane of abiochip and single pore insertions number of active cells, andsequencing yield were compared to those obtained using polymerasecomplexes present in the unenriched mixture of the standard Eintofmethod.

The number of inserted nanopores (single pore insertions) obtained bythe positive isolation method, was compared to the number of poreinsertions obtained using the standard. Eintof mixture of unenrichedfractions when complexed with the GAD template substrate or the JAM1A.The results are shown in FIG. 11 and Table 1A.

The number of active cells obtained by the positive isolation method,was compared to the number of pore insertions obtained using thestandard. Eintof mixture of unenriched fractions when complexed with theGAD template substrate or the JAM1A. The results are shown in FIG. 12and Table 1B.

The percent sequencing yield measured as a percent of active cells ofthe total number of cells (6143) present on the, was compared to thepercent sequencing yield obtained using the standard. Eintof mixture ofunenriched fractions when complexed with the GAD template substrate orthe JAM1A. The results are shown in FIG. 13 and Table 1C. The samplecomprising the polymerase complexes enriched by the positive isolationmethod showed an increase of about 2.3 times that obtained using thestandard mixture Eintof method.

A summary of the data is provided in Table 2.

An example of the current trace obtained using the isolated polymerasecomplexes is given in FIG. 14 . Tags of the tagged nucleotidesincorporated into a template dependent DNA strand are shown in green,black, blue and red. The method used for sequencing using tags isdescribed in PCT/US2013/068967 (entitled “Nucleic Acid Sequencing UsingTags” filed on Nov. 7, 2013, which is herein incorporated by referencein its entirety).

The data show that the number of pore insertions, the number of activecells, and the percent sequencing yield obtained using fractionsenriched in polymerase complexes obtained by the positive isolationmethod described herein were at least 100% greater than the sameparameters measured for polymerase complexes obtained in mixturesprovided by the standard Eintof method.

TABLE 1A Num- Std. Lower Upper ber Mean * Error 95% 95% Enrichedpositive 32 490.000 46.46 397.56 582.44 isolation method (GAD template)Standard unenriched 27 238.778 50.5877 138.14 339.41 Eintof method (GADtemplate) Standard unenriched 26 190.346 51.551 87.80 292.90 Eintofmethod (JAM1A template) * Means for Oneway Anova

TABLE 1B Num- Std. Lower Upper ber Mean* Error 95% 95% Enriched positive32 83.9063 8.4863 67.024 100.79 isolation method (GAD template) Standardunenriched 27 34.8519 9.2387 16.473 53.23 Eintof method (GAD template)Standard unenriched 26 37.5000 9.4147 18.771 56.23 Eintof method (JAM1Atemplate) *Means for Oneway Anova

TABLE 1C Num- Std. Lower Upper ber Mean* Error 95% 95% Enriched positive32 1.36587 013816 1.0910 1.6407 isolation method (GAD template) Standardunenriched 27 0.56726 0.15041 0.2681 0.8665 Eintof method (GAD template)Standard unenriched 26 0.61038 0.15327 0.3055 0.9153 Eintof method(JAM1A template) *Means for Oneway Anova

TABLE 2 Standard Standard unenriched unenriched Enriched positive EintofEintof isolation method method (GAD method (JAM1A (GAD template)template) template) Total # stations 32 27 26 Avg. Single pores 490 239190 Avg. Active cells 84 35 38 Avg % Seq Yield 1.366 0.528 0.635 (6143electrodes)

Example 3

Negative Enrichment—Isolation of Polymerase Complexes

This example relates to a method for purifying a nanopore sequencingcomplex, or a polymerase complex, by negatively isolating the desiredcomplexes i.e. nanopore sequencing complex, or a polymerase complex froma mixture of complex components. The complex components are positivelyisolated by attaching them to a solid phase support, leaving the desiredcomplexes in the unbound fraction.

A schematic of the process is provided in FIG. 7 .

CITATION LIST Patent Literature

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The invention claimed is:
 1. A method for isolating active polymerasecomplexes, wherein the method comprises the following steps: (a)providing a reaction mixture comprising: (i) a polymerase enzyme,wherein the polymerase enzyme is either active or inactive, (ii) asingle-stranded polynucleotide template, and (iii) a captureoligonucleotide conjugated to a purification moiety, wherein the captureoligonucleotide hybridizes to a portion of the polynucleotide template,wherein the polynucleotide template is a self-priming template thatgenerates a self-complementary sequence that acts as a primer fortemplate-dependent extension by the polymerase enzyme, thereby formingpolymerase complexes, wherein the polymerase complex comprises a complexof: (i) a polymerase enzyme, and (ii) a single-stranded polynucleotidetemplate; (b) binding the polymerase complexes to a solid phase support,wherein the solid phase support comprises a purification moiety-bindingcompound, by binding of the purification moiety-binding compound of thesolid phase support with the purification moiety of the captureoligonucleotide; (c) providing reagents comprising nucleotides forenabling template-dependent extension by an active polymerase enzyme,wherein the self-priming template of the polynucleotide templategenerates a self-complementary sequence that acts as a primer fortemplate-dependent extension by the active polymerase, therebygenerating a plurality of the active polymerase complexes comprisingextended complementary sequences; and (d) isolating (i) the activepolymerase complexes having extended complementary sequences from (ii)the inactive polymerase complexes comprising unextended complementarysequences, thereby isolating said active polymerase complexes from saidpolymerase complex components, wherein the inactive polymerase complexeshaving unextended complementary sequences remain bound to said solidphase support, and the active polymerase complexes having extendedcomplementary sequences are released from the solid phase support by theactivity of the active polymerase enzyme.
 2. The method of claim 1,wherein the polynucleotide template is a linear or a circular template,and wherein the reaction mixtures of step (a) each further comprise anoligonucleotide primer.
 3. The method of claim 1, further comprisingremoving active polymerase complexes that are not bound to the solidphase support from the inactive polymerase complexes that are bound tothe solid phase support.
 4. The method of claim 1, wherein thepurification moiety is a biotin or modified biotin, and the purificationmoiety-binding compound is streptavidin or modified streptavidin.
 5. Themethod of claim 4, wherein the biotin or modified biotin isdesthiobiotin or a derivative thereof.
 6. The method of claim 1, whereinthe polymerase complex further comprises a nanopore.
 7. A method forpositively isolating a polymerase complex, wherein the polymerasecomplex comprises a complex of: (i) a polymerase enzyme, (ii) apolynucleotide template, and (iii) a capture oligonucleotide, whereineach capture oligonucleotide comprises a purification moiety, whereinthe capture oligonucleotide hybridizes to a portion of thepolynucleotide template due to complementarity, and wherein methodcomprises the following steps: (a) providing a reaction mixturecomprising a plurality of polymerase enzymes, a plurality ofpolynucleotide templates, and a plurality of capture oligonucleotides,wherein each capture oligonucleotide comprising a purification moiety,thereby enabling the formation of a plurality of polymerase complexes,wherein a polymerase complex is formed only when a polymerase enzymeassociates with a capture oligonucleotide that is hybridized to aportion of the polynucleotide template due to complementarity; (b)binding the plurality of polymerase complexes formed in step (a) to asolid phase support, wherein the solid phase support comprises apurification moiety-binding compound; and (c) removing the polymeraseenzymes, polynucleotide templates, and capture oligonucleotides that arenot bound to the solid phase support from the polymerase complexes thatare bound to the solid phase support, thereby positively isolatingpolymerase complexes.
 8. The method of claim 7, wherein thepolynucleotide template is a linear or a continuous template, andwherein the capture oligonucleotide is a capture oligonucleotide primer.9. The method of claim 7, further comprising a step of step (d)releasing polymerase complexes from the solid phase support.
 10. Themethod of claim 7, wherein the purification moiety is a biotin ormodified biotin, and the purification moiety-binding compound isstreptavidin or modified streptavidin.
 11. The method of claim 10,wherein the biotin or modified biotin is desthiobiotin or a derivativethereof.
 12. The method of claim 7, wherein the isolated polymerasecomplex further comprises a nanopore.